Last updated on 2026-02-03 14:51:26 CET.
| Flavor | Version | Tinstall | Tcheck | Ttotal | Status | Flags |
|---|---|---|---|---|---|---|
| r-devel-linux-x86_64-debian-clang | 0.3.7 | 6.43 | 165.36 | 171.79 | NOTE | |
| r-devel-linux-x86_64-debian-gcc | 0.3.7 | 4.38 | 114.13 | 118.51 | NOTE | |
| r-devel-linux-x86_64-fedora-clang | 0.3.7 | 10.00 | 268.00 | 278.00 | ERROR | |
| r-devel-linux-x86_64-fedora-gcc | 0.3.7 | 11.00 | 275.40 | 286.40 | ERROR | |
| r-devel-windows-x86_64 | 0.3.7 | 10.00 | 185.00 | 195.00 | OK | |
| r-patched-linux-x86_64 | 0.3.7 | 7.00 | 155.36 | 162.36 | OK | |
| r-release-linux-x86_64 | 0.3.7 | 6.38 | 156.31 | 162.69 | OK | |
| r-release-macos-arm64 | 0.3.7 | OK | ||||
| r-release-macos-x86_64 | 0.3.7 | 4.00 | 199.00 | 203.00 | OK | |
| r-release-windows-x86_64 | 0.3.7 | 10.00 | 182.00 | 192.00 | OK | |
| r-oldrel-macos-arm64 | 0.3.7 | OK | ||||
| r-oldrel-macos-x86_64 | 0.3.7 | 4.00 | 196.00 | 200.00 | OK | |
| r-oldrel-windows-x86_64 | 0.3.7 | 14.00 | 231.00 | 245.00 | OK |
Version: 0.3.7
Check: relative paths in package URLs
Result: NOTE
Found the following (possibly) invalid URL:
URL: ../reference/
From: inst/doc/comprehensive-guide.html
Flavors: r-devel-linux-x86_64-debian-clang, r-devel-linux-x86_64-debian-gcc
Version: 0.3.7
Check: tests
Result: ERROR
Running ‘testthat.R’ [83s/118s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
> # This file is part of the standard setup for testthat.
> # It is recommended that you do not modify it.
> #
> # Where should you do additional test configuration?
> # Learn more about the roles of various files in:
> # * https://r-pkgs.org/testing-design.html#sec-tests-files-overview
> # * https://testthat.r-lib.org/articles/special-files.html
>
> library(testthat)
> library(evanverse)
>
> test_check("evanverse")
x RDS file not found: '/tmp/RtmpbgoPKw/working_dir/RtmpNcw1Ej/file206e133321ee4e.rds'
v Installed: stats
v Installed: cli
v Installed: ggplot2
v Installed: stats
v Installed: utils
-- Compiling Color Palettes (JSON \u2192 RDS) ----------------------------------
v Added 'demo_palette' (Type: qualitative, 2 colors)
v Saved RDS: /tmp/RtmpbgoPKw/working_dir/RtmpNcw1Ej/file206e1374c90e57.rds
-- Compilation Summary --
i Sequential: 0
i Diverging: 0
i Qualitative: 1
v All palettes compiled successfully!
-- Compiling Color Palettes (JSON \u2192 RDS) ----------------------------------
! Failed to parse JSON: /tmp/RtmpbgoPKw/working_dir/RtmpNcw1Ej/palettes_206e137f886e9/qualitative/invalid.json
v Saved RDS: /tmp/RtmpbgoPKw/working_dir/RtmpNcw1Ej/file206e132180f969.rds
-- Compilation Summary --
i Sequential: 0
i Diverging: 0
i Qualitative: 0
v All palettes compiled successfully!
-- Compiling Color Palettes (JSON \u2192 RDS) ----------------------------------
! Missing fields (colors) in: /tmp/RtmpbgoPKw/working_dir/RtmpNcw1Ej/palettes_206e13423eb58d/qualitative/incomplete.json
v Saved RDS: /tmp/RtmpbgoPKw/working_dir/RtmpNcw1Ej/file206e132bc0346c.rds
-- Compilation Summary --
i Sequential: 0
i Diverging: 0
i Qualitative: 0
v All palettes compiled successfully!
-- Compiling Color Palettes (JSON \u2192 RDS) ----------------------------------
v Added 'seq_pal' (Type: sequential, 2 colors)
v Added 'div_pal' (Type: diverging, 2 colors)
v Saved RDS: /tmp/RtmpbgoPKw/working_dir/RtmpNcw1Ej/file206e137e3755d4.rds
-- Compilation Summary --
i Sequential: 1
i Diverging: 1
i Qualitative: 0
v All palettes compiled successfully!
i Converting symbols to UPPERCASE (human standard)
i Creating standardized column: symbol_upper
i Creating standardized column: symbol_lower
i Converting symbols to UPPERCASE (human standard)
i Converting symbols to UPPERCASE (human standard)
i Directory created: /tmp/RtmpbgoPKw/working_dir/RtmpNcw1Ej/palette_test_206e1333369a5a/qualitative
v Palette saved: /tmp/RtmpbgoPKw/working_dir/RtmpNcw1Ej/palette_test_206e1333369a5a/qualitative/testset.json
i Directory created: /tmp/RtmpbgoPKw/working_dir/RtmpNcw1Ej/reuse_test_206e13502611d4/diverging
v Palette saved: /tmp/RtmpbgoPKw/working_dir/RtmpNcw1Ej/reuse_test_206e13502611d4/diverging/reused.json
! Palette already exists: /tmp/RtmpbgoPKw/working_dir/RtmpNcw1Ej/reuse_test_206e13502611d4/diverging/reused.json
i Directory created: /tmp/RtmpbgoPKw/working_dir/RtmpNcw1Ej/log_test_206e134d5e7a7d/qualitative
v Palette saved: /tmp/RtmpbgoPKw/working_dir/RtmpNcw1Ej/log_test_206e134d5e7a7d/qualitative/logtest.json
-- Directory Tree: /tmp/RtmpbgoPKw/working_dir/RtmpNcw1Ej/file206e137d4bc9d3 ---
+-- test.txt
-- Directory Tree: /tmp/RtmpbgoPKw/working_dir/RtmpNcw1Ej/file206e1319303cd9 ---
+-- file1.txt
+-- subdir
+-- file2.txt
-- Directory Tree: /tmp/RtmpbgoPKw/working_dir/RtmpNcw1Ej/file206e1354906e8f ---
+-- level1
-- Directory Tree: /tmp/RtmpbgoPKw/working_dir/RtmpNcw1Ej/file206e1354906e8f ---
+-- level1
+-- level2
+-- deep_file.txt
-- Directory Tree: /tmp/RtmpbgoPKw/working_dir/RtmpNcw1Ej/file206e1363dd7afc ---
+-- example.txt
v File tree log saved to: /tmp/RtmpbgoPKw/working_dir/RtmpNcw1Ej/file206e1363dd7afc/logs/tree/test.log
-- Directory Tree: /tmp/RtmpbgoPKw/working_dir/RtmpNcw1Ej/file206e132ea906de ---
+-- sample.txt
v File tree log saved to: /tmp/RtmpbgoPKw/working_dir/RtmpNcw1Ej/file206e132ea906de/logs/content_test.log
-- Directory Tree: /tmp/RtmpbgoPKw/working_dir/RtmpNcw1Ej/file206e133cb081dd ---
+-- test.txt
v File tree log saved to: /tmp/RtmpbgoPKw/working_dir/RtmpNcw1Ej/file206e133cb081dd/logs/file_tree_20260203_125727.log
-- Directory Tree: /tmp/RtmpbgoPKw/working_dir/RtmpNcw1Ej/file206e131419a36 ----
+-- file1.txt
v File tree log saved to: /tmp/RtmpbgoPKw/working_dir/RtmpNcw1Ej/file206e1328e10fb6/overwrite_test.log
-- Directory Tree: /tmp/RtmpbgoPKw/working_dir/RtmpNcw1Ej/file206e131419a36 ----
+-- file1.txt
v File tree log saved to: /tmp/RtmpbgoPKw/working_dir/RtmpNcw1Ej/file206e1328e10fb6/overwrite_test.log
-- Directory Tree: /tmp/RtmpbgoPKw/working_dir/RtmpNcw1Ej/file206e132923f24 ----
+-- file1.txt
v File tree log saved to: /tmp/RtmpbgoPKw/working_dir/RtmpNcw1Ej/file206e133ab4afad/append_test.log
-- Directory Tree: /tmp/RtmpbgoPKw/working_dir/RtmpNcw1Ej/file206e132923f24 ----
+-- file1.txt
v File tree log saved to: /tmp/RtmpbgoPKw/working_dir/RtmpNcw1Ej/file206e133ab4afad/append_test.log
x Directory does not exist: nonexistent/directory/path
-- Directory Tree: /tmp/RtmpbgoPKw/working_dir/RtmpNcw1Ej/file206e13174a06e6 ---
-- Directory Tree: /tmp/RtmpbgoPKw/working_dir/RtmpNcw1Ej/file206e13560dd8f6 ---
+-- test.txt
v File tree log saved to: /tmp/RtmpbgoPKw/working_dir/RtmpNcw1Ej/file206e13560dd8f6/new/log/path/test.log
v Loaded palette "vividset" ("qualitative"), 9 colors
v Loaded palette "vividset" ("qualitative"), 9 colors
v Loaded palette "vividset" ("qualitative"), 9 colors
i #FF8000 -> RGB: c(255, 128, 0)
i #00FF00 -> RGB: c(0, 255, 0)
i Mapping completed for 'id': 1 unmatched value(s) assigned to default.
i Mapping completed for 'id': 1 unmatched value(s) assigned to default.
i Mapping completed for 'group': 1 unmatched value(s) assigned to default.
i Mapping completed for 'id': 1 unmatched value(s) assigned to default.
-- Objects are NOT identical ---------------------------------------------------
x Type mismatch: integer vs double
x Class mismatch: integer vs numeric
x Values differ at 1 position(s), e.g., index 3: 3 vs 4
-- Objects are NOT identical ---------------------------------------------------
x Values differ at 1 position(s), e.g., index 2: b vs c
-- Objects are NOT identical ---------------------------------------------------
x Type mismatch: integer vs double
x Values differ at 1 cell(s), e.g., [2,2]: 4 vs 5
-- Objects are NOT identical ---------------------------------------------------
x Values differ in column 'y' at 1 row(s), e.g., row 2: b vs c
-- Objects are NOT identical ---------------------------------------------------
x Names differ: a, b vs b, a
x Values differ at 2 position(s), e.g., index 1: 1 vs 2
-- Objects are NOT identical ---------------------------------------------------
x Column names differ: x, y vs y, x
-- Objects are NOT identical ---------------------------------------------------
x Dimnames differ: (r1|r2; c1|c2) vs (r1|r2; cX|c2)
-- Objects are NOT identical ---------------------------------------------------
-- Objects are NOT identical ---------------------------------------------------
-- Objects are NOT identical ---------------------------------------------------
x Dimension mismatch: 0x0 vs 1x0
-- Objects are NOT identical ---------------------------------------------------
x Length mismatch: 2 vs 3
-- Objects are NOT identical ---------------------------------------------------
x Dimension mismatch: 2x2 vs 1x4
-- Objects are NOT identical ---------------------------------------------------
x Column names differ: x vs y
x Unsupported type for 'a': list
x Unsupported type for 'b': function
! Large n (25) may cause numeric overflow. Consider using the 'gmp' package for arbitrary precision.
! Large n (171) may cause numeric overflow. Consider using the 'gmp' package for arbitrary precision.
-- Package: stats --
i Matched exported names: 461
.MFclass
.checkMFClasses
.getXlevels
.lm.fit
.nknots.smspl
.preformat.ts
.vcov.aliased
AIC
ARMAacf
ARMAtoMA
BIC
Box.test
C
D
DF2formula
Gamma
HoltWinters
IQR
KalmanForecast
KalmanLike
KalmanRun
KalmanSmooth
NLSstAsymptotic
NLSstClosestX
NLSstLfAsymptote
NLSstRtAsymptote
PP.test
Pair
SSD
SSasymp
SSasympOff
SSasympOrig
SSbiexp
SSfol
SSfpl
SSgompertz
SSlogis
SSmicmen
SSweibull
StructTS
TukeyHSD
acf
acf2AR
add.scope
add1
addmargins
aggregate
aggregate.data.frame
aggregate.ts
alias
anova
ansari.test
aov
approx
approxfun
ar
ar.burg
ar.mle
ar.ols
ar.yw
arima
arima.sim
arima0
arima0.diag
as.dendrogram
as.dist
as.formula
as.hclust
as.stepfun
as.ts
asOneSidedFormula
ave
bandwidth.kernel
bartlett.test
binom.test
binomial
biplot
bw.SJ
bw.bcv
bw.nrd
bw.nrd0
bw.ucv
cancor
case.names
ccf
chisq.test
cmdscale
coef
coefficients
complete.cases
confint
confint.default
confint.lm
constrOptim
contr.SAS
contr.helmert
contr.poly
contr.sum
contr.treatment
contrasts
contrasts<-
convolve
cooks.distance
cophenetic
cor
cor.test
cov
cov.wt
cov2cor
covratio
cpgram
cutree
cycle
dbeta
dbinom
dcauchy
dchisq
decompose
delete.response
deltat
dendrapply
density
density.default
deriv
deriv3
deviance
dexp
df
df.kernel
df.residual
dfbeta
dfbetas
dffits
dgamma
dgeom
dhyper
diffinv
dist
dlnorm
dlogis
dmultinom
dnbinom
dnorm
dpois
drop.scope
drop.terms
drop1
dsignrank
dt
dummy.coef
dummy.coef.lm
dunif
dweibull
dwilcox
ecdf
eff.aovlist
effects
embed
end
estVar
expand.model.frame
extractAIC
factanal
factor.scope
family
fft
filter
fisher.test
fitted
fitted.values
fivenum
fligner.test
formula
frequency
friedman.test
ftable
gaussian
getCall
getInitial
get_all_vars
glm
glm.control
glm.fit
hasTsp
hat
hatvalues
hclust
heatmap
influence
influence.measures
integrate
interaction.plot
inverse.gaussian
is.empty.model
is.leaf
is.mts
is.stepfun
is.ts
is.tskernel
isoreg
kernapply
kernel
kmeans
knots
kruskal.test
ks.test
ksmooth
lag
lag.plot
line
lm
lm.fit
lm.influence
lm.wfit
loadings
loess
loess.control
loess.smooth
logLik
loglin
lowess
ls.diag
ls.print
lsfit
mad
mahalanobis
make.link
makeARIMA
makepredictcall
manova
mantelhaen.test
mauchly.test
mcnemar.test
median
median.default
medpolish
model.extract
model.frame
model.frame.default
model.matrix
model.matrix.default
model.matrix.lm
model.offset
model.response
model.tables
model.weights
monthplot
mood.test
mvfft
na.action
na.contiguous
na.exclude
na.fail
na.omit
na.pass
napredict
naprint
naresid
nextn
nlm
nlminb
nls
nls.control
nobs
numericDeriv
offset
oneway.test
optim
optimHess
optimise
optimize
order.dendrogram
p.adjust
p.adjust.methods
pacf
pairwise.prop.test
pairwise.t.test
pairwise.table
pairwise.wilcox.test
pbeta
pbinom
pbirthday
pcauchy
pchisq
pexp
pf
pgamma
pgeom
phyper
plclust
plnorm
plogis
plot.ecdf
plot.spec.coherency
plot.spec.phase
plot.stepfun
plot.ts
pnbinom
pnorm
poisson
poisson.test
poly
polym
power
power.anova.test
power.prop.test
power.t.test
ppoints
ppois
ppr
prcomp
predict
predict.glm
predict.lm
preplot
princomp
printCoefmat
profile
proj
promax
prop.test
prop.trend.test
psignrank
psmirnov
pt
ptukey
punif
pweibull
pwilcox
qbeta
qbinom
qbirthday
qcauchy
qchisq
qexp
qf
qgamma
qgeom
qhyper
qlnorm
qlogis
qnbinom
qnorm
qpois
qqline
qqnorm
qqplot
qr.influence
qsignrank
qsmirnov
qt
qtukey
quade.test
quantile
quasi
quasibinomial
quasipoisson
qunif
qweibull
qwilcox
r2dtable
rWishart
rbeta
rbinom
rcauchy
rchisq
read.ftable
rect.hclust
reformulate
relevel
reorder
replications
reshape
resid
residuals
residuals.glm
residuals.lm
rexp
rf
rgamma
rgeom
rhyper
rlnorm
rlogis
rmultinom
rnbinom
rnorm
rpois
rsignrank
rsmirnov
rstandard
rstudent
rt
runif
runmed
rweibull
rwilcox
scatter.smooth
screeplot
sd
se.contrast
selfStart
setNames
shapiro.test
sigma
simulate
smooth
smooth.spline
smoothEnds
sortedXyData
spec.ar
spec.pgram
spec.taper
spectrum
spline
splinefun
splinefunH
start
stat.anova
step
stepfun
stl
summary.aov
summary.glm
summary.lm
summary.manova
summary.stepfun
supsmu
symnum
t.test
termplot
terms
terms.formula
time
toeplitz
toeplitz2
ts
ts.intersect
ts.plot
ts.union
tsSmooth
tsdiag
tsp
tsp<-
uniroot
update
update.default
update.formula
var
var.test
variable.names
varimax
vcov
weighted.mean
weighted.residuals
weights
wilcox.test
window
window<-
write.ftable
xtabs
-- Package: stats --
i Matched exported names: 461
.MFclass
.checkMFClasses
.getXlevels
.lm.fit
.nknots.smspl
.preformat.ts
.vcov.aliased
AIC
ARMAacf
ARMAtoMA
BIC
Box.test
C
D
DF2formula
Gamma
HoltWinters
IQR
KalmanForecast
KalmanLike
KalmanRun
KalmanSmooth
NLSstAsymptotic
NLSstClosestX
NLSstLfAsymptote
NLSstRtAsymptote
PP.test
Pair
SSD
SSasymp
SSasympOff
SSasympOrig
SSbiexp
SSfol
SSfpl
SSgompertz
SSlogis
SSmicmen
SSweibull
StructTS
TukeyHSD
acf
acf2AR
add.scope
add1
addmargins
aggregate
aggregate.data.frame
aggregate.ts
alias
anova
ansari.test
aov
approx
approxfun
ar
ar.burg
ar.mle
ar.ols
ar.yw
arima
arima.sim
arima0
arima0.diag
as.dendrogram
as.dist
as.formula
as.hclust
as.stepfun
as.ts
asOneSidedFormula
ave
bandwidth.kernel
bartlett.test
binom.test
binomial
biplot
bw.SJ
bw.bcv
bw.nrd
bw.nrd0
bw.ucv
cancor
case.names
ccf
chisq.test
cmdscale
coef
coefficients
complete.cases
confint
confint.default
confint.lm
constrOptim
contr.SAS
contr.helmert
contr.poly
contr.sum
contr.treatment
contrasts
contrasts<-
convolve
cooks.distance
cophenetic
cor
cor.test
cov
cov.wt
cov2cor
covratio
cpgram
cutree
cycle
dbeta
dbinom
dcauchy
dchisq
decompose
delete.response
deltat
dendrapply
density
density.default
deriv
deriv3
deviance
dexp
df
df.kernel
df.residual
dfbeta
dfbetas
dffits
dgamma
dgeom
dhyper
diffinv
dist
dlnorm
dlogis
dmultinom
dnbinom
dnorm
dpois
drop.scope
drop.terms
drop1
dsignrank
dt
dummy.coef
dummy.coef.lm
dunif
dweibull
dwilcox
ecdf
eff.aovlist
effects
embed
end
estVar
expand.model.frame
extractAIC
factanal
factor.scope
family
fft
filter
fisher.test
fitted
fitted.values
fivenum
fligner.test
formula
frequency
friedman.test
ftable
gaussian
getCall
getInitial
get_all_vars
glm
glm.control
glm.fit
hasTsp
hat
hatvalues
hclust
heatmap
influence
influence.measures
integrate
interaction.plot
inverse.gaussian
is.empty.model
is.leaf
is.mts
is.stepfun
is.ts
is.tskernel
isoreg
kernapply
kernel
kmeans
knots
kruskal.test
ks.test
ksmooth
lag
lag.plot
line
lm
lm.fit
lm.influence
lm.wfit
loadings
loess
loess.control
loess.smooth
logLik
loglin
lowess
ls.diag
ls.print
lsfit
mad
mahalanobis
make.link
makeARIMA
makepredictcall
manova
mantelhaen.test
mauchly.test
mcnemar.test
median
median.default
medpolish
model.extract
model.frame
model.frame.default
model.matrix
model.matrix.default
model.matrix.lm
model.offset
model.response
model.tables
model.weights
monthplot
mood.test
mvfft
na.action
na.contiguous
na.exclude
na.fail
na.omit
na.pass
napredict
naprint
naresid
nextn
nlm
nlminb
nls
nls.control
nobs
numericDeriv
offset
oneway.test
optim
optimHess
optimise
optimize
order.dendrogram
p.adjust
p.adjust.methods
pacf
pairwise.prop.test
pairwise.t.test
pairwise.table
pairwise.wilcox.test
pbeta
pbinom
pbirthday
pcauchy
pchisq
pexp
pf
pgamma
pgeom
phyper
plclust
plnorm
plogis
plot.ecdf
plot.spec.coherency
plot.spec.phase
plot.stepfun
plot.ts
pnbinom
pnorm
poisson
poisson.test
poly
polym
power
power.anova.test
power.prop.test
power.t.test
ppoints
ppois
ppr
prcomp
predict
predict.glm
predict.lm
preplot
princomp
printCoefmat
profile
proj
promax
prop.test
prop.trend.test
psignrank
psmirnov
pt
ptukey
punif
pweibull
pwilcox
qbeta
qbinom
qbirthday
qcauchy
qchisq
qexp
qf
qgamma
qgeom
qhyper
qlnorm
qlogis
qnbinom
qnorm
qpois
qqline
qqnorm
qqplot
qr.influence
qsignrank
qsmirnov
qt
qtukey
quade.test
quantile
quasi
quasibinomial
quasipoisson
qunif
qweibull
qwilcox
r2dtable
rWishart
rbeta
rbinom
rcauchy
rchisq
read.ftable
rect.hclust
reformulate
relevel
reorder
replications
reshape
resid
residuals
residuals.glm
residuals.lm
rexp
rf
rgamma
rgeom
rhyper
rlnorm
rlogis
rmultinom
rnbinom
rnorm
rpois
rsignrank
rsmirnov
rstandard
rstudent
rt
runif
runmed
rweibull
rwilcox
scatter.smooth
screeplot
sd
se.contrast
selfStart
setNames
shapiro.test
sigma
simulate
smooth
smooth.spline
smoothEnds
sortedXyData
spec.ar
spec.pgram
spec.taper
spectrum
spline
splinefun
splinefunH
start
stat.anova
step
stepfun
stl
summary.aov
summary.glm
summary.lm
summary.manova
summary.stepfun
supsmu
symnum
t.test
termplot
terms
terms.formula
time
toeplitz
toeplitz2
ts
ts.intersect
ts.plot
ts.union
tsSmooth
tsdiag
tsp
tsp<-
uniroot
update
update.default
update.formula
var
var.test
variable.names
varimax
vcov
weighted.mean
weighted.residuals
weights
wilcox.test
window
window<-
write.ftable
xtabs
-- Package: stats --
i Matched exported names: 24
.lm.fit
KalmanForecast
KalmanLike
KalmanRun
KalmanSmooth
confint.lm
contr.helmert
dummy.coef.lm
glm
glm.control
glm.fit
lm
lm.fit
lm.influence
lm.wfit
model.matrix.lm
nlm
nlminb
predict.glm
predict.lm
residuals.glm
residuals.lm
summary.glm
summary.lm
-- Package: stats --
i Matched exported names: 24
.lm.fit
KalmanForecast
KalmanLike
KalmanRun
KalmanSmooth
confint.lm
contr.helmert
dummy.coef.lm
glm
glm.control
glm.fit
lm
lm.fit
lm.influence
lm.wfit
model.matrix.lm
nlm
nlminb
predict.glm
predict.lm
residuals.glm
residuals.lm
summary.glm
summary.lm
-- Package: stats --
i Matched exported names: 0
! No exported names matched keyword: zzzzzz
Saving _problems/test-plot_pie-69.R
Saving _problems/test-plot_pie-75.R
Saving _problems/test-plot_pie-97.R
Saving _problems/test-plot_pie-97.R
Saving _problems/test-plot_pie-97.R
Saving _problems/test-plot_pie-97.R
Saving _problems/test-plot_pie-135.R
Saving _problems/test-plot_pie-146.R
i s1 had 74 duplicates, now de-duplicated.
i s2 had 94 duplicates, now de-duplicated.
i s1 had 74 duplicates, now de-duplicated.
i s2 had 94 duplicates, now de-duplicated.
i a had 27 duplicates, now de-duplicated.
i b had 19 duplicates, now de-duplicated.
v Loaded palette "vividset" ("qualitative"), 9 colors
v Loaded palette "vividset" ("qualitative"), 9 colors
v Loaded palette "vividset" ("qualitative"), 9 colors
v Loaded palette "vividset" ("qualitative"), 9 colors
v Loaded palette "vividset" ("qualitative"), 9 colors
v Loaded palette "vividset" ("qualitative"), 9 colors
-- Reading Excel file --
i Sheets in '/tmp/RtmpbgoPKw/working_dir/RtmpNcw1Ej/file206e133a9beb35.xlsx': Sheet1
v Column names cleaned with janitor::clean_names().
v Successfully read sheet 1 from '/tmp/RtmpbgoPKw/working_dir/RtmpNcw1Ej/file206e133a9beb35.xlsx'.
-- Reading Excel file --
i Sheets in '/tmp/RtmpbgoPKw/working_dir/RtmpNcw1Ej/file206e133c3f0426.xlsx': Sheet1
v Column names cleaned with janitor::clean_names().
v Successfully read sheet 1 from '/tmp/RtmpbgoPKw/working_dir/RtmpNcw1Ej/file206e133c3f0426.xlsx'.
-- Reading Excel file --
i Sheets in '/tmp/RtmpbgoPKw/working_dir/RtmpNcw1Ej/file206e13360ff6a.xlsx': Sheet1
v Successfully read sheet 1 from '/tmp/RtmpbgoPKw/working_dir/RtmpNcw1Ej/file206e13360ff6a.xlsx'.
-- Reading Excel file --
i Sheets in '/tmp/RtmpbgoPKw/working_dir/RtmpNcw1Ej/file206e1326980e7e.xlsx': Sheet1
v Column names cleaned with janitor::clean_names().
v Successfully read sheet 1 from '/tmp/RtmpbgoPKw/working_dir/RtmpNcw1Ej/file206e1326980e7e.xlsx'.
Path: '/tmp/RtmpbgoPKw/working_dir/RtmpNcw1Ej/file206e13530896e.csv'
Separator: "," | Encoding: "UTF-8"
OpenMP version (_OPENMP) 202011
omp_get_num_procs() 24
R_DATATABLE_NUM_PROCS_PERCENT unset (default 50)
R_DATATABLE_NUM_THREADS unset
R_DATATABLE_THROTTLE unset (default 1024)
omp_get_thread_limit() 2
omp_get_max_threads() 24
OMP_THREAD_LIMIT 2
OMP_NUM_THREADS unset
RestoreAfterFork true
data.table is using 2 threads with throttle==1024. See ?setDTthreads.
freadR.c has been passed a filename: /tmp/RtmpbgoPKw/working_dir/RtmpNcw1Ej/file206e13530896e.csv
[01] Check arguments
Using 2 threads (omp_get_max_threads()=24, nth=2)
NAstrings = [<<NA>>]
None of the NAstrings look like numbers.
show progress = 1
0/1 column will be read as integer
Y/N column will be read as character
[02] Opening the file
Opening file /tmp/RtmpbgoPKw/working_dir/RtmpNcw1Ej/file206e13530896e.csv
File opened, size = 235 bytes.
Memory mapped ok
[03] Detect and skip BOM
[04] Arrange mmap to be \0 terminated
\n has been found in the input (counts: 0 \r by themselves vs 6 [\r]*\n) and different lines can end with different line endings (e.g. mixed \n and \r\n in one file). This is common and ideal.
[05] Skipping initial rows if needed
Positioned on line 1 starting: <<mpg,cyl,disp,hp,drat,wt,qsec,v>>
[06] Detect separator, quoting rule, and ncolumns
Using supplied sep ','
sep=',' with 6 lines of 11 fields using quote rule 0
Detected 11 columns on line 1. This line is either column names or first data row. Line starts as: <<mpg,cyl,disp,hp,drat,wt,qsec,v>>
Quote rule picked = 0
fill=false and the most number of columns found is 11
[07] Detect column types, dec, good nrow estimate and whether first row is column names
'header' changed by user from 'auto' to true
sep=',' so dec set to '.'
Number of sampling jump points = 1 because (234 bytes from row 1 to eof) / (2 * 234 jump0size) == 0
Type codes (jump 000) : 97779997777 Quote rule 0
All rows were sampled since file is small so we know nrow=5 exactly
[08] Assign column names
[09] Apply user overrides on column types
After 0 type and 0 drop user overrides : 97779997777
[10] Allocate memory for the datatable
Allocating 11 column slots (11 - 0 dropped) with 5 rows
[11] Read the data
jumps=[0..1), chunk_size=1048576, total_size=189
Read 5 rows x 11 columns from 235 bytes file in 00:00.000 wall clock time
[12] Finalizing the datatable
Type counts:
7 : int32 '7'
4 : float64 '9'
=============================
0.000s ( 41%) Memory map 0.000GiB file
0.000s ( 38%) sep=',' ncol=11 and header detection
0.000s ( 5%) Column type detection using 5 sample rows
0.000s ( 4%) Allocation of 5 rows x 11 cols (0.000GiB) of which 5 (100%) rows used
0.000s ( 12%) Reading 1 chunks (0 swept) of 1.000MiB (each chunk 5 rows) using 1 threads
+ 0.000s ( 1%) Parse to row-major thread buffers (grown 0 times)
+ 0.000s ( 0%) Transpose
+ 0.000s ( 10%) Waiting
0.000s ( 0%) Rereading 0 columns due to out-of-sample type exceptions
0.000s Total
v File loaded successfully (5 rows \u00d7 11 cols)
-- glimpse
`glimpse(df)` from dplyr/tibble gives a compact overview.
-- glimpse
`glimpse(df)` from dplyr/tibble gives a compact overview.
-- read_excel
`readxl::read_excel("yourfile.xlsx")` reads Excel files. Supports `sheet =`, `range =`, etc.
-- glimpse
`glimpse(df)` from dplyr/tibble gives a compact overview.
-- Usage Examples --------------------------------------------------------------
-- glimpse
`glimpse(df)` from dplyr/tibble gives a compact overview.
-- read_excel
`readxl::read_excel("yourfile.xlsx")` reads Excel files. Supports `sheet =`, `range =`, etc.
-- droplevels
`droplevels(df)` removes unused factor levels from a data frame or factor.
-- modifyList
`modifyList(x, y)` merges two lists; elements in `y` overwrite those in `x`.
-- do.call
`do.call(fun, args)` calls a function with arguments in a list: `do.call(plot, list(x = 1:10))`.
-- sprintf
`sprintf("Hello, %s!", name)` formats strings with `%s`, `%d`, etc.
-- scRNAseq
`scRNAseq` (Bioconductor) provides scRNA-seq datasets, e.g., `ZeiselBrainData()`.
-- basename
`basename(path)` extracts the filename from a full path. See also `dirname()`.
-- here
`here::here("data", "raw", "sample1.rds")` builds a path from project root.
-- stopifnot
`stopifnot(cond1, cond2, ...)` throws if any condition is FALSE.
-- object.size
`object.size(x)` estimates memory size; use `format()` to pretty-print.
-- slice
`slice(df, 1:3)` selects rows by position; see `slice_head()`, `slice_tail()`, `slice_max()`.
-- unzip
`unzip("file.zip", exdir = "dir")` extracts ZIP archives.
-- gunzip
`R.utils::gunzip("file.csv.gz", remove = FALSE)` decompresses .gz files.
-- untar
`untar("file.tar.gz", exdir = "dir")` extracts .tar or .tar.gz archives.
-- NoLegend
`NoLegend()` removes legends from ggplot2/Seurat plots.
-- RotatedAxis
`RotatedAxis()` rotates x-axis text for readability in dot plots.
-- guides
`guides(fill = "none")` customizes or removes legends (with `scale_*`).
-- log2
`log2(x)` base-2 logarithm (often for fold change).
-- log
`log(x, base = exp(1))` natural log by default; set `base = 10` or `2` for others.
-- log10
`log10(x)` base-10 logarithm (orders of magnitude).
-- round
`round(x, digits = 0)` rounds; use `signif()` for significant digits.
-- floor
`floor(x)` greatest integer ≤ x (e.g., `floor(2.8)` -> 2).
-- ceiling
`ceiling(x)` smallest integer ≥ x (e.g., `ceiling(2.1)` -> 3).
-- cut
`cut(x, breaks)` bins numeric vector; `breaks = 3` or custom; `labels = FALSE` for group indices.
-- cumsum
`cumsum(x)` cumulative sum.
-- cumprod
`cumprod(x)` cumulative product.
-- cummin
`cummin(x)` running minimum.
-- cummax
`cummax(x)` running maximum.
-- row_number
`row_number(x)` order rank (ties broken arbitrarily).
-- min_rank
`min_rank(x)` ties get the same minimum rank.
-- dense_rank
`dense_rank(x)` like `min_rank()` but without gaps.
-- percent_rank
`percent_rank(x)` relative rank in [0,1], normalized by n-1.
-- cume_dist
`cume_dist(x)` cumulative proportion of values ≤ x.
-- str_view
`stringr::str_view(string, pattern)` highlights regex matches; `str_view_all()` for all.
-- str_c
`stringr::str_c(...)` concatenates; use `sep`/`collapse` as needed.
-- str_glue
`glue::glue("Hello, {name}!")` inline expressions with `{}`.
-- str_flatten
`stringr::str_flatten(x, collapse = ", ")` join a character vector.
-- str_length
`stringr::str_length(x)` string lengths.
-- str_sub
`stringr::str_sub(x, start, end)` extract/replace substrings (supports negative indices).
-- today
`lubridate::today()` current Date (no time).
-- now
`lubridate::now()` current POSIXct date-time.
-- Sys.timezone
`Sys.timezone()` system time zone name.
-- skimr
`skimr::skim(df)` compact, readable data summaries.
-- par
`par(mfrow = c(m, n))` split plotting area (e.g., 2x2).
-- layout
`layout(matrix, widths, heights)` flexible plot arrangement.
-- datatable
`DT::datatable(data)` interactive table (search/filter/sort/paginate).
-- windowsFonts
`windowsFonts()` register system fonts (Windows).
-- sign
`sign(x)` returns -1/0/1 for negative/zero/positive.
-- reactable
`reactable::reactable(data)` modern interactive table.
-- trimws
`trimws(x)` removes leading and trailing whitespace.
-- Available Keywords ----------------------------------------------------------
`glimpse, read_excel, droplevels, modifyList, do.call, sprintf, scRNAseq,
basename, here, stopifnot, object.size, slice, unzip, gunzip, untar, NoLegend,
RotatedAxis, guides, log2, log, log10, round, floor, ceiling, cut, cumsum,
cumprod, cummin, cummax, row_number, min_rank, dense_rank, percent_rank,
cume_dist, str_view, str_c, str_glue, str_flatten, str_length, str_sub, today,
now, Sys.timezone, skimr, par, layout, datatable, windowsFonts, sign,
reactable, trimws`
x No match found for keyword: "notakeyword"
-- min_rank
`min_rank(x)` ties get the same minimum rank.
-- dense_rank
`dense_rank(x)` like `min_rank()` but without gaps.
-- percent_rank
`percent_rank(x)` relative rank in [0,1], normalized by n-1.
v Palette removed from qualitative: '/tmp/RtmpbgoPKw/working_dir/RtmpNcw1Ej/palettes_test_206e13b0199e/qualitative/test_palette.json'
! Palette not found in any type: nonexistent
v Palette removed from diverging: '/tmp/RtmpbgoPKw/working_dir/RtmpNcw1Ej/palettes_test_206e1353ad5f69/diverging/test_palette.json'
v Palette removed from qualitative: '/tmp/RtmpbgoPKw/working_dir/RtmpNcw1Ej/custom_palettes_206e131e61569a/qualitative/custom_test.json'
v RGB: c(255, 128, 0) → HEX: #FF8000
v RGB: c(0, 0, 0) → HEX: #000000
v RGB: c(255, 255, 255) → HEX: #FFFFFF
v Converted 3 RGB values to HEX.
i RGB: c(255, 128, 0) → HEX: #FF8000
i RGB: c(0, 255, 0) → HEX: #00FF00
i RGB: c(0, 0, 255) → HEX: #0000FF
v RGB: c(0, 1, 255) → HEX: #0001FF
x An error occurred: non-numeric argument to mathematical function
-- Setting cran mirror --
v CRAN mirror set to: <https://mirrors.tuna.tsinghua.edu.cn/CRAN>
i Available CRAN mirrors: "official", "rstudio", "tuna", "ustc", "aliyun", "sjtu", "pku", "hku", "westlake", "nju", and "sustech"
i View current settings: `getOption('repos')` & `getOption('BioC_mirror')`
-- Setting cran mirror --
v CRAN mirror set to: <https://mirrors.ustc.edu.cn/CRAN>
i Available CRAN mirrors: "official", "rstudio", "tuna", "ustc", "aliyun", "sjtu", "pku", "hku", "westlake", "nju", and "sustech"
i View current settings: `getOption('repos')` & `getOption('BioC_mirror')`
-- Setting cran mirror --
v CRAN mirror set to: <https://mirrors.westlake.edu.cn/CRAN>
i Available CRAN mirrors: "official", "rstudio", "tuna", "ustc", "aliyun", "sjtu", "pku", "hku", "westlake", "nju", and "sustech"
i View current settings: `getOption('repos')` & `getOption('BioC_mirror')`
-- Setting bioc mirror --
v Bioconductor mirror set to: <https://mirrors.tuna.tsinghua.edu.cn/bioconductor>
i Available Bioc mirrors: "official", "tuna", "ustc", "westlake", and "nju"
i View current settings: `getOption('repos')` & `getOption('BioC_mirror')`
-- Setting bioc mirror --
v Bioconductor mirror set to: <https://mirrors.ustc.edu.cn/bioconductor>
i Available Bioc mirrors: "official", "tuna", "ustc", "westlake", and "nju"
i View current settings: `getOption('repos')` & `getOption('BioC_mirror')`
-- Setting bioc mirror --
v Bioconductor mirror set to: <https://mirrors.westlake.edu.cn/bioconductor>
i Available Bioc mirrors: "official", "tuna", "ustc", "westlake", and "nju"
i View current settings: `getOption('repos')` & `getOption('BioC_mirror')`
-- Setting all mirror --
v CRAN mirror set to: <https://mirrors.tuna.tsinghua.edu.cn/CRAN>
v Bioconductor mirror set to: <https://mirrors.tuna.tsinghua.edu.cn/bioconductor>
i Available CRAN mirrors: "official", "rstudio", "tuna", "ustc", "aliyun", "sjtu", "pku", "hku", "westlake", "nju", and "sustech"
i Available Bioc mirrors: "official", "tuna", "ustc", "westlake", and "nju"
i View current settings: `getOption('repos')` & `getOption('BioC_mirror')`
-- Setting all mirror --
v CRAN mirror set to: <https://mirrors.ustc.edu.cn/CRAN>
v Bioconductor mirror set to: <https://mirrors.ustc.edu.cn/bioconductor>
i Available CRAN mirrors: "official", "rstudio", "tuna", "ustc", "aliyun", "sjtu", "pku", "hku", "westlake", "nju", and "sustech"
i Available Bioc mirrors: "official", "tuna", "ustc", "westlake", and "nju"
i View current settings: `getOption('repos')` & `getOption('BioC_mirror')`
-- Setting cran mirror --
-- Setting bioc mirror --
-- Setting cran mirror --
v CRAN mirror set to: <https://mirrors.tuna.tsinghua.edu.cn/CRAN>
i Available CRAN mirrors: "official", "rstudio", "tuna", "ustc", "aliyun", "sjtu", "pku", "hku", "westlake", "nju", and "sustech"
i View current settings: `getOption('repos')` & `getOption('BioC_mirror')`
-- Setting all mirror --
v CRAN mirror set to: <https://mirrors.tuna.tsinghua.edu.cn/CRAN>
v Bioconductor mirror set to: <https://mirrors.tuna.tsinghua.edu.cn/bioconductor>
i Available CRAN mirrors: "official", "rstudio", "tuna", "ustc", "aliyun", "sjtu", "pku", "hku", "westlake", "nju", and "sustech"
i Available Bioc mirrors: "official", "tuna", "ustc", "westlake", and "nju"
i View current settings: `getOption('repos')` & `getOption('BioC_mirror')`
-- Setting cran mirror --
i Available CRAN mirrors: "official", "rstudio", "tuna", "ustc", "aliyun", "sjtu", "pku", "hku", "westlake", "nju", and "sustech"
i View current settings: `getOption('repos')` & `getOption('BioC_mirror')`
-- Setting bioc mirror --
i Available Bioc mirrors: "official", "tuna", "ustc", "westlake", and "nju"
i View current settings: `getOption('repos')` & `getOption('BioC_mirror')`
-- Setting cran mirror --
v CRAN mirror set to: <https://mirrors.tuna.tsinghua.edu.cn/CRAN>
i View current settings: `getOption('repos')` & `getOption('BioC_mirror')`
-- Setting cran mirror --
v CRAN mirror set to: <https://mirrors.tuna.tsinghua.edu.cn/CRAN>
i Available CRAN mirrors: "official", "rstudio", "tuna", "ustc", "aliyun", "sjtu", "pku", "hku", "westlake", "nju", and "sustech"
-- Setting cran mirror --
v CRAN mirror set to: <https://mirrors.tuna.tsinghua.edu.cn/CRAN>
i Available CRAN mirrors: "official", "rstudio", "tuna", "ustc", "aliyun", "sjtu", "pku", "hku", "westlake", "nju", and "sustech"
i View current settings: `getOption('repos')` & `getOption('BioC_mirror')`
-- Setting bioc mirror --
-- Setting all mirror --
-- Setting cran mirror --
v CRAN mirror set to: <https://cloud.r-project.org>
i Available CRAN mirrors: "official", "rstudio", "tuna", "ustc", "aliyun", "sjtu", "pku", "hku", "westlake", "nju", and "sustech"
i View current settings: `getOption('repos')` & `getOption('BioC_mirror')`
-- Setting bioc mirror --
v Bioconductor mirror set to: <https://bioconductor.org>
i Available Bioc mirrors: "official", "tuna", "ustc", "westlake", and "nju"
i View current settings: `getOption('repos')` & `getOption('BioC_mirror')`
i Square test started at 2026-02-03 12:58:41
v Square test completed in 0.001 seconds
i Silent task started at 2026-02-03 12:58:41
v Silent task completed in 0.000 seconds
v Excel file written to '/tmp/RtmpbgoPKw/working_dir/RtmpNcw1Ej/file206e135d89eecc.xlsx'
v Excel file written to '/tmp/RtmpbgoPKw/working_dir/RtmpNcw1Ej/file206e1382042a7.xlsx'
v Excel file written to '/tmp/RtmpbgoPKw/working_dir/RtmpNcw1Ej/file206e13146684d6.xlsx'
! File already exists and will be overwritten: '/tmp/RtmpbgoPKw/working_dir/RtmpNcw1Ej/file206e13146684d6.xlsx'
v Excel file written to '/tmp/RtmpbgoPKw/working_dir/RtmpNcw1Ej/file206e13146684d6.xlsx'
v Excel file written to '/tmp/RtmpbgoPKw/working_dir/RtmpNcw1Ej/test-write-206e1390a7a4d_2026-02-03.xlsx'
[ FAIL 8 | WARN 5 | SKIP 44 | PASS 1310 ]
══ Skipped tests (44) ══════════════════════════════════════════════════════════
• On CRAN (44): 'test-check_pkg.R:48:3', 'test-download_batch.R:19:3',
'test-download_batch.R:39:3', 'test-download_gene_ref.R:20:3',
'test-download_gene_ref.R:31:3', 'test-download_gene_ref.R:42:3',
'test-download_gene_ref.R:55:3', 'test-download_geo_data.R:11:3',
'test-download_geo_data.R:21:3', 'test-download_geo_data.R:50:3',
'test-download_geo_data.R:61:3', 'test-download_geo_data.R:80:3',
'test-download_geo_data.R:101:3', 'test-download_geo_data.R:155:3',
'test-download_geo_data.R:178:3', 'test-download_geo_data.R:208:3',
'test-download_url.R:10:3', 'test-download_url.R:22:3',
'test-download_url.R:39:3', 'test-download_url.R:103:3',
'test-download_url.R:117:3', 'test-download_url.R:147:3',
'test-download_url.R:177:3', 'test-download_url.R:205:3',
'test-download_url.R:227:3', 'test-download_url.R:252:3',
'test-download_url.R:279:3', 'test-download_url.R:306:3',
'test-file_info.R:12:3', 'test-file_info.R:26:3', 'test-file_info.R:48:3',
'test-file_info.R:59:3', 'test-file_info.R:71:3', 'test-pkg_version.R:19:3',
'test-pkg_version.R:27:3', 'test-pkg_version.R:37:3',
'test-pkg_version.R:48:3', 'test-plot_forest.R:11:3',
'test-plot_forest.R:32:3', 'test-plot_forest.R:53:3',
'test-plot_forest.R:71:3', 'test-plot_forest.R:93:3',
'test-plot_forest.R:119:3', 'test-plot_forest.R:140:3'
══ Failed tests ════════════════════════════════════════════════════════════════
── Failure ('test-plot_pie.R:69:3'): plot_pie() works with character vector input ──
Expected `p <- plot_pie(vec, preview = FALSE)` to run silently.
Actual noise: warnings.
── Failure ('test-plot_pie.R:75:3'): plot_pie() works with data.frame input ────
Expected `p <- plot_pie(df, group_col = "group", count_col = "count", preview = FALSE)` to run silently.
Actual noise: warnings.
── Failure ('test-plot_pie.R:97:5'): plot_pie() handles different label types ──
Expected `p <- plot_pie(df, label = lbl, preview = FALSE)` to run silently.
Actual noise: warnings.
── Failure ('test-plot_pie.R:97:5'): plot_pie() handles different label types ──
Expected `p <- plot_pie(df, label = lbl, preview = FALSE)` to run silently.
Actual noise: warnings.
── Failure ('test-plot_pie.R:97:5'): plot_pie() handles different label types ──
Expected `p <- plot_pie(df, label = lbl, preview = FALSE)` to run silently.
Actual noise: warnings.
── Failure ('test-plot_pie.R:97:5'): plot_pie() handles different label types ──
Expected `p <- plot_pie(df, label = lbl, preview = FALSE)` to run silently.
Actual noise: warnings.
── Failure ('test-plot_pie.R:135:3'): plot_pie() handles custom colors ─────────
Expected `p <- plot_pie(df, fill = custom_colors, preview = FALSE)` to run silently.
Actual noise: warnings.
── Failure ('test-plot_pie.R:141:3'): plot_pie() handles custom title and colors ──
Expected `... <- NULL` to run silently.
Actual noise: warnings.
[ FAIL 8 | WARN 5 | SKIP 44 | PASS 1310 ]
Error:
! Test failures.
Execution halted
Flavor: r-devel-linux-x86_64-fedora-clang
Version: 0.3.7
Check: tests
Result: ERROR
Running ‘testthat.R’ [77s/147s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
> # This file is part of the standard setup for testthat.
> # It is recommended that you do not modify it.
> #
> # Where should you do additional test configuration?
> # Learn more about the roles of various files in:
> # * https://r-pkgs.org/testing-design.html#sec-tests-files-overview
> # * https://testthat.r-lib.org/articles/special-files.html
>
> library(testthat)
> library(evanverse)
>
> test_check("evanverse")
x RDS file not found: '/tmp/RtmpmL9GWn/working_dir/RtmpyQLugc/file1ac42317525c50.rds'
v Installed: stats
v Installed: cli
v Installed: ggplot2
v Installed: stats
v Installed: utils
-- Compiling Color Palettes (JSON \u2192 RDS) ----------------------------------
v Added 'demo_palette' (Type: qualitative, 2 colors)
v Saved RDS: /tmp/RtmpmL9GWn/working_dir/RtmpyQLugc/file1ac4231887ce7d.rds
-- Compilation Summary --
i Sequential: 0
i Diverging: 0
i Qualitative: 1
v All palettes compiled successfully!
-- Compiling Color Palettes (JSON \u2192 RDS) ----------------------------------
! Failed to parse JSON: /tmp/RtmpmL9GWn/working_dir/RtmpyQLugc/palettes_1ac42311b68969/qualitative/invalid.json
v Saved RDS: /tmp/RtmpmL9GWn/working_dir/RtmpyQLugc/file1ac4237b4e75df.rds
-- Compilation Summary --
i Sequential: 0
i Diverging: 0
i Qualitative: 0
v All palettes compiled successfully!
-- Compiling Color Palettes (JSON \u2192 RDS) ----------------------------------
! Missing fields (colors) in: /tmp/RtmpmL9GWn/working_dir/RtmpyQLugc/palettes_1ac4232b910268/qualitative/incomplete.json
v Saved RDS: /tmp/RtmpmL9GWn/working_dir/RtmpyQLugc/file1ac42321b25682.rds
-- Compilation Summary --
i Sequential: 0
i Diverging: 0
i Qualitative: 0
v All palettes compiled successfully!
-- Compiling Color Palettes (JSON \u2192 RDS) ----------------------------------
v Added 'seq_pal' (Type: sequential, 2 colors)
v Added 'div_pal' (Type: diverging, 2 colors)
v Saved RDS: /tmp/RtmpmL9GWn/working_dir/RtmpyQLugc/file1ac423304f1599.rds
-- Compilation Summary --
i Sequential: 1
i Diverging: 1
i Qualitative: 0
v All palettes compiled successfully!
i Converting symbols to UPPERCASE (human standard)
i Creating standardized column: symbol_upper
i Creating standardized column: symbol_lower
i Converting symbols to UPPERCASE (human standard)
i Converting symbols to UPPERCASE (human standard)
i Directory created: /tmp/RtmpmL9GWn/working_dir/RtmpyQLugc/palette_test_1ac42376760dbb/qualitative
v Palette saved: /tmp/RtmpmL9GWn/working_dir/RtmpyQLugc/palette_test_1ac42376760dbb/qualitative/testset.json
i Directory created: /tmp/RtmpmL9GWn/working_dir/RtmpyQLugc/reuse_test_1ac4235b5035a3/diverging
v Palette saved: /tmp/RtmpmL9GWn/working_dir/RtmpyQLugc/reuse_test_1ac4235b5035a3/diverging/reused.json
! Palette already exists: /tmp/RtmpmL9GWn/working_dir/RtmpyQLugc/reuse_test_1ac4235b5035a3/diverging/reused.json
i Directory created: /tmp/RtmpmL9GWn/working_dir/RtmpyQLugc/log_test_1ac423b895c3d/qualitative
v Palette saved: /tmp/RtmpmL9GWn/working_dir/RtmpyQLugc/log_test_1ac423b895c3d/qualitative/logtest.json
-- Directory Tree: /tmp/RtmpmL9GWn/working_dir/RtmpyQLugc/file1ac42358432a46 ---
+-- test.txt
-- Directory Tree: /tmp/RtmpmL9GWn/working_dir/RtmpyQLugc/file1ac4235a915d97 ---
+-- file1.txt
+-- subdir
+-- file2.txt
-- Directory Tree: /tmp/RtmpmL9GWn/working_dir/RtmpyQLugc/file1ac423368db562 ---
+-- level1
-- Directory Tree: /tmp/RtmpmL9GWn/working_dir/RtmpyQLugc/file1ac423368db562 ---
+-- level1
+-- level2
+-- deep_file.txt
-- Directory Tree: /tmp/RtmpmL9GWn/working_dir/RtmpyQLugc/file1ac42376f220dc ---
+-- example.txt
v File tree log saved to: /tmp/RtmpmL9GWn/working_dir/RtmpyQLugc/file1ac42376f220dc/logs/tree/test.log
-- Directory Tree: /tmp/RtmpmL9GWn/working_dir/RtmpyQLugc/file1ac423379fb7d8 ---
+-- sample.txt
v File tree log saved to: /tmp/RtmpmL9GWn/working_dir/RtmpyQLugc/file1ac423379fb7d8/logs/content_test.log
-- Directory Tree: /tmp/RtmpmL9GWn/working_dir/RtmpyQLugc/file1ac4233b5bc349 ---
+-- test.txt
v File tree log saved to: /tmp/RtmpmL9GWn/working_dir/RtmpyQLugc/file1ac4233b5bc349/logs/file_tree_20260203_120317.log
-- Directory Tree: /tmp/RtmpmL9GWn/working_dir/RtmpyQLugc/file1ac423452e388d ---
+-- file1.txt
v File tree log saved to: /tmp/RtmpmL9GWn/working_dir/RtmpyQLugc/file1ac4233d30f778/overwrite_test.log
-- Directory Tree: /tmp/RtmpmL9GWn/working_dir/RtmpyQLugc/file1ac423452e388d ---
+-- file1.txt
v File tree log saved to: /tmp/RtmpmL9GWn/working_dir/RtmpyQLugc/file1ac4233d30f778/overwrite_test.log
-- Directory Tree: /tmp/RtmpmL9GWn/working_dir/RtmpyQLugc/file1ac42310a2e433 ---
+-- file1.txt
v File tree log saved to: /tmp/RtmpmL9GWn/working_dir/RtmpyQLugc/file1ac4234f890208/append_test.log
-- Directory Tree: /tmp/RtmpmL9GWn/working_dir/RtmpyQLugc/file1ac42310a2e433 ---
+-- file1.txt
v File tree log saved to: /tmp/RtmpmL9GWn/working_dir/RtmpyQLugc/file1ac4234f890208/append_test.log
x Directory does not exist: nonexistent/directory/path
-- Directory Tree: /tmp/RtmpmL9GWn/working_dir/RtmpyQLugc/file1ac4237700d822 ---
-- Directory Tree: /tmp/RtmpmL9GWn/working_dir/RtmpyQLugc/file1ac42348b4e74a ---
+-- test.txt
v File tree log saved to: /tmp/RtmpmL9GWn/working_dir/RtmpyQLugc/file1ac42348b4e74a/new/log/path/test.log
v Loaded palette "vividset" ("qualitative"), 9 colors
v Loaded palette "vividset" ("qualitative"), 9 colors
v Loaded palette "vividset" ("qualitative"), 9 colors
i #FF8000 -> RGB: c(255, 128, 0)
i #00FF00 -> RGB: c(0, 255, 0)
i Mapping completed for 'id': 1 unmatched value(s) assigned to default.
i Mapping completed for 'id': 1 unmatched value(s) assigned to default.
i Mapping completed for 'group': 1 unmatched value(s) assigned to default.
i Mapping completed for 'id': 1 unmatched value(s) assigned to default.
-- Objects are NOT identical ---------------------------------------------------
x Type mismatch: integer vs double
x Class mismatch: integer vs numeric
x Values differ at 1 position(s), e.g., index 3: 3 vs 4
-- Objects are NOT identical ---------------------------------------------------
x Values differ at 1 position(s), e.g., index 2: b vs c
-- Objects are NOT identical ---------------------------------------------------
x Type mismatch: integer vs double
x Values differ at 1 cell(s), e.g., [2,2]: 4 vs 5
-- Objects are NOT identical ---------------------------------------------------
x Values differ in column 'y' at 1 row(s), e.g., row 2: b vs c
-- Objects are NOT identical ---------------------------------------------------
x Names differ: a, b vs b, a
x Values differ at 2 position(s), e.g., index 1: 1 vs 2
-- Objects are NOT identical ---------------------------------------------------
x Column names differ: x, y vs y, x
-- Objects are NOT identical ---------------------------------------------------
x Dimnames differ: (r1|r2; c1|c2) vs (r1|r2; cX|c2)
-- Objects are NOT identical ---------------------------------------------------
-- Objects are NOT identical ---------------------------------------------------
-- Objects are NOT identical ---------------------------------------------------
x Dimension mismatch: 0x0 vs 1x0
-- Objects are NOT identical ---------------------------------------------------
x Length mismatch: 2 vs 3
-- Objects are NOT identical ---------------------------------------------------
x Dimension mismatch: 2x2 vs 1x4
-- Objects are NOT identical ---------------------------------------------------
x Column names differ: x vs y
x Unsupported type for 'a': list
x Unsupported type for 'b': function
! Large n (25) may cause numeric overflow. Consider using the 'gmp' package for arbitrary precision.
! Large n (171) may cause numeric overflow. Consider using the 'gmp' package for arbitrary precision.
-- Package: stats --
i Matched exported names: 461
.MFclass
.checkMFClasses
.getXlevels
.lm.fit
.nknots.smspl
.preformat.ts
.vcov.aliased
AIC
ARMAacf
ARMAtoMA
BIC
Box.test
C
D
DF2formula
Gamma
HoltWinters
IQR
KalmanForecast
KalmanLike
KalmanRun
KalmanSmooth
NLSstAsymptotic
NLSstClosestX
NLSstLfAsymptote
NLSstRtAsymptote
PP.test
Pair
SSD
SSasymp
SSasympOff
SSasympOrig
SSbiexp
SSfol
SSfpl
SSgompertz
SSlogis
SSmicmen
SSweibull
StructTS
TukeyHSD
acf
acf2AR
add.scope
add1
addmargins
aggregate
aggregate.data.frame
aggregate.ts
alias
anova
ansari.test
aov
approx
approxfun
ar
ar.burg
ar.mle
ar.ols
ar.yw
arima
arima.sim
arima0
arima0.diag
as.dendrogram
as.dist
as.formula
as.hclust
as.stepfun
as.ts
asOneSidedFormula
ave
bandwidth.kernel
bartlett.test
binom.test
binomial
biplot
bw.SJ
bw.bcv
bw.nrd
bw.nrd0
bw.ucv
cancor
case.names
ccf
chisq.test
cmdscale
coef
coefficients
complete.cases
confint
confint.default
confint.lm
constrOptim
contr.SAS
contr.helmert
contr.poly
contr.sum
contr.treatment
contrasts
contrasts<-
convolve
cooks.distance
cophenetic
cor
cor.test
cov
cov.wt
cov2cor
covratio
cpgram
cutree
cycle
dbeta
dbinom
dcauchy
dchisq
decompose
delete.response
deltat
dendrapply
density
density.default
deriv
deriv3
deviance
dexp
df
df.kernel
df.residual
dfbeta
dfbetas
dffits
dgamma
dgeom
dhyper
diffinv
dist
dlnorm
dlogis
dmultinom
dnbinom
dnorm
dpois
drop.scope
drop.terms
drop1
dsignrank
dt
dummy.coef
dummy.coef.lm
dunif
dweibull
dwilcox
ecdf
eff.aovlist
effects
embed
end
estVar
expand.model.frame
extractAIC
factanal
factor.scope
family
fft
filter
fisher.test
fitted
fitted.values
fivenum
fligner.test
formula
frequency
friedman.test
ftable
gaussian
getCall
getInitial
get_all_vars
glm
glm.control
glm.fit
hasTsp
hat
hatvalues
hclust
heatmap
influence
influence.measures
integrate
interaction.plot
inverse.gaussian
is.empty.model
is.leaf
is.mts
is.stepfun
is.ts
is.tskernel
isoreg
kernapply
kernel
kmeans
knots
kruskal.test
ks.test
ksmooth
lag
lag.plot
line
lm
lm.fit
lm.influence
lm.wfit
loadings
loess
loess.control
loess.smooth
logLik
loglin
lowess
ls.diag
ls.print
lsfit
mad
mahalanobis
make.link
makeARIMA
makepredictcall
manova
mantelhaen.test
mauchly.test
mcnemar.test
median
median.default
medpolish
model.extract
model.frame
model.frame.default
model.matrix
model.matrix.default
model.matrix.lm
model.offset
model.response
model.tables
model.weights
monthplot
mood.test
mvfft
na.action
na.contiguous
na.exclude
na.fail
na.omit
na.pass
napredict
naprint
naresid
nextn
nlm
nlminb
nls
nls.control
nobs
numericDeriv
offset
oneway.test
optim
optimHess
optimise
optimize
order.dendrogram
p.adjust
p.adjust.methods
pacf
pairwise.prop.test
pairwise.t.test
pairwise.table
pairwise.wilcox.test
pbeta
pbinom
pbirthday
pcauchy
pchisq
pexp
pf
pgamma
pgeom
phyper
plclust
plnorm
plogis
plot.ecdf
plot.spec.coherency
plot.spec.phase
plot.stepfun
plot.ts
pnbinom
pnorm
poisson
poisson.test
poly
polym
power
power.anova.test
power.prop.test
power.t.test
ppoints
ppois
ppr
prcomp
predict
predict.glm
predict.lm
preplot
princomp
printCoefmat
profile
proj
promax
prop.test
prop.trend.test
psignrank
psmirnov
pt
ptukey
punif
pweibull
pwilcox
qbeta
qbinom
qbirthday
qcauchy
qchisq
qexp
qf
qgamma
qgeom
qhyper
qlnorm
qlogis
qnbinom
qnorm
qpois
qqline
qqnorm
qqplot
qr.influence
qsignrank
qsmirnov
qt
qtukey
quade.test
quantile
quasi
quasibinomial
quasipoisson
qunif
qweibull
qwilcox
r2dtable
rWishart
rbeta
rbinom
rcauchy
rchisq
read.ftable
rect.hclust
reformulate
relevel
reorder
replications
reshape
resid
residuals
residuals.glm
residuals.lm
rexp
rf
rgamma
rgeom
rhyper
rlnorm
rlogis
rmultinom
rnbinom
rnorm
rpois
rsignrank
rsmirnov
rstandard
rstudent
rt
runif
runmed
rweibull
rwilcox
scatter.smooth
screeplot
sd
se.contrast
selfStart
setNames
shapiro.test
sigma
simulate
smooth
smooth.spline
smoothEnds
sortedXyData
spec.ar
spec.pgram
spec.taper
spectrum
spline
splinefun
splinefunH
start
stat.anova
step
stepfun
stl
summary.aov
summary.glm
summary.lm
summary.manova
summary.stepfun
supsmu
symnum
t.test
termplot
terms
terms.formula
time
toeplitz
toeplitz2
ts
ts.intersect
ts.plot
ts.union
tsSmooth
tsdiag
tsp
tsp<-
uniroot
update
update.default
update.formula
var
var.test
variable.names
varimax
vcov
weighted.mean
weighted.residuals
weights
wilcox.test
window
window<-
write.ftable
xtabs
-- Package: stats --
i Matched exported names: 461
.MFclass
.checkMFClasses
.getXlevels
.lm.fit
.nknots.smspl
.preformat.ts
.vcov.aliased
AIC
ARMAacf
ARMAtoMA
BIC
Box.test
C
D
DF2formula
Gamma
HoltWinters
IQR
KalmanForecast
KalmanLike
KalmanRun
KalmanSmooth
NLSstAsymptotic
NLSstClosestX
NLSstLfAsymptote
NLSstRtAsymptote
PP.test
Pair
SSD
SSasymp
SSasympOff
SSasympOrig
SSbiexp
SSfol
SSfpl
SSgompertz
SSlogis
SSmicmen
SSweibull
StructTS
TukeyHSD
acf
acf2AR
add.scope
add1
addmargins
aggregate
aggregate.data.frame
aggregate.ts
alias
anova
ansari.test
aov
approx
approxfun
ar
ar.burg
ar.mle
ar.ols
ar.yw
arima
arima.sim
arima0
arima0.diag
as.dendrogram
as.dist
as.formula
as.hclust
as.stepfun
as.ts
asOneSidedFormula
ave
bandwidth.kernel
bartlett.test
binom.test
binomial
biplot
bw.SJ
bw.bcv
bw.nrd
bw.nrd0
bw.ucv
cancor
case.names
ccf
chisq.test
cmdscale
coef
coefficients
complete.cases
confint
confint.default
confint.lm
constrOptim
contr.SAS
contr.helmert
contr.poly
contr.sum
contr.treatment
contrasts
contrasts<-
convolve
cooks.distance
cophenetic
cor
cor.test
cov
cov.wt
cov2cor
covratio
cpgram
cutree
cycle
dbeta
dbinom
dcauchy
dchisq
decompose
delete.response
deltat
dendrapply
density
density.default
deriv
deriv3
deviance
dexp
df
df.kernel
df.residual
dfbeta
dfbetas
dffits
dgamma
dgeom
dhyper
diffinv
dist
dlnorm
dlogis
dmultinom
dnbinom
dnorm
dpois
drop.scope
drop.terms
drop1
dsignrank
dt
dummy.coef
dummy.coef.lm
dunif
dweibull
dwilcox
ecdf
eff.aovlist
effects
embed
end
estVar
expand.model.frame
extractAIC
factanal
factor.scope
family
fft
filter
fisher.test
fitted
fitted.values
fivenum
fligner.test
formula
frequency
friedman.test
ftable
gaussian
getCall
getInitial
get_all_vars
glm
glm.control
glm.fit
hasTsp
hat
hatvalues
hclust
heatmap
influence
influence.measures
integrate
interaction.plot
inverse.gaussian
is.empty.model
is.leaf
is.mts
is.stepfun
is.ts
is.tskernel
isoreg
kernapply
kernel
kmeans
knots
kruskal.test
ks.test
ksmooth
lag
lag.plot
line
lm
lm.fit
lm.influence
lm.wfit
loadings
loess
loess.control
loess.smooth
logLik
loglin
lowess
ls.diag
ls.print
lsfit
mad
mahalanobis
make.link
makeARIMA
makepredictcall
manova
mantelhaen.test
mauchly.test
mcnemar.test
median
median.default
medpolish
model.extract
model.frame
model.frame.default
model.matrix
model.matrix.default
model.matrix.lm
model.offset
model.response
model.tables
model.weights
monthplot
mood.test
mvfft
na.action
na.contiguous
na.exclude
na.fail
na.omit
na.pass
napredict
naprint
naresid
nextn
nlm
nlminb
nls
nls.control
nobs
numericDeriv
offset
oneway.test
optim
optimHess
optimise
optimize
order.dendrogram
p.adjust
p.adjust.methods
pacf
pairwise.prop.test
pairwise.t.test
pairwise.table
pairwise.wilcox.test
pbeta
pbinom
pbirthday
pcauchy
pchisq
pexp
pf
pgamma
pgeom
phyper
plclust
plnorm
plogis
plot.ecdf
plot.spec.coherency
plot.spec.phase
plot.stepfun
plot.ts
pnbinom
pnorm
poisson
poisson.test
poly
polym
power
power.anova.test
power.prop.test
power.t.test
ppoints
ppois
ppr
prcomp
predict
predict.glm
predict.lm
preplot
princomp
printCoefmat
profile
proj
promax
prop.test
prop.trend.test
psignrank
psmirnov
pt
ptukey
punif
pweibull
pwilcox
qbeta
qbinom
qbirthday
qcauchy
qchisq
qexp
qf
qgamma
qgeom
qhyper
qlnorm
qlogis
qnbinom
qnorm
qpois
qqline
qqnorm
qqplot
qr.influence
qsignrank
qsmirnov
qt
qtukey
quade.test
quantile
quasi
quasibinomial
quasipoisson
qunif
qweibull
qwilcox
r2dtable
rWishart
rbeta
rbinom
rcauchy
rchisq
read.ftable
rect.hclust
reformulate
relevel
reorder
replications
reshape
resid
residuals
residuals.glm
residuals.lm
rexp
rf
rgamma
rgeom
rhyper
rlnorm
rlogis
rmultinom
rnbinom
rnorm
rpois
rsignrank
rsmirnov
rstandard
rstudent
rt
runif
runmed
rweibull
rwilcox
scatter.smooth
screeplot
sd
se.contrast
selfStart
setNames
shapiro.test
sigma
simulate
smooth
smooth.spline
smoothEnds
sortedXyData
spec.ar
spec.pgram
spec.taper
spectrum
spline
splinefun
splinefunH
start
stat.anova
step
stepfun
stl
summary.aov
summary.glm
summary.lm
summary.manova
summary.stepfun
supsmu
symnum
t.test
termplot
terms
terms.formula
time
toeplitz
toeplitz2
ts
ts.intersect
ts.plot
ts.union
tsSmooth
tsdiag
tsp
tsp<-
uniroot
update
update.default
update.formula
var
var.test
variable.names
varimax
vcov
weighted.mean
weighted.residuals
weights
wilcox.test
window
window<-
write.ftable
xtabs
-- Package: stats --
i Matched exported names: 24
.lm.fit
KalmanForecast
KalmanLike
KalmanRun
KalmanSmooth
confint.lm
contr.helmert
dummy.coef.lm
glm
glm.control
glm.fit
lm
lm.fit
lm.influence
lm.wfit
model.matrix.lm
nlm
nlminb
predict.glm
predict.lm
residuals.glm
residuals.lm
summary.glm
summary.lm
-- Package: stats --
i Matched exported names: 24
.lm.fit
KalmanForecast
KalmanLike
KalmanRun
KalmanSmooth
confint.lm
contr.helmert
dummy.coef.lm
glm
glm.control
glm.fit
lm
lm.fit
lm.influence
lm.wfit
model.matrix.lm
nlm
nlminb
predict.glm
predict.lm
residuals.glm
residuals.lm
summary.glm
summary.lm
-- Package: stats --
i Matched exported names: 0
! No exported names matched keyword: zzzzzz
Saving _problems/test-plot_pie-69.R
Saving _problems/test-plot_pie-75.R
Saving _problems/test-plot_pie-97.R
Saving _problems/test-plot_pie-97.R
Saving _problems/test-plot_pie-97.R
Saving _problems/test-plot_pie-97.R
Saving _problems/test-plot_pie-135.R
Saving _problems/test-plot_pie-146.R
i s1 had 74 duplicates, now de-duplicated.
i s2 had 94 duplicates, now de-duplicated.
i s1 had 74 duplicates, now de-duplicated.
i s2 had 94 duplicates, now de-duplicated.
i a had 27 duplicates, now de-duplicated.
i b had 19 duplicates, now de-duplicated.
v Loaded palette "vividset" ("qualitative"), 9 colors
v Loaded palette "vividset" ("qualitative"), 9 colors
v Loaded palette "vividset" ("qualitative"), 9 colors
v Loaded palette "vividset" ("qualitative"), 9 colors
v Loaded palette "vividset" ("qualitative"), 9 colors
v Loaded palette "vividset" ("qualitative"), 9 colors
-- Reading Excel file --
i Sheets in '/tmp/RtmpmL9GWn/working_dir/RtmpyQLugc/file1ac423128af7bb.xlsx': Sheet1
v Column names cleaned with janitor::clean_names().
v Successfully read sheet 1 from '/tmp/RtmpmL9GWn/working_dir/RtmpyQLugc/file1ac423128af7bb.xlsx'.
-- Reading Excel file --
i Sheets in '/tmp/RtmpmL9GWn/working_dir/RtmpyQLugc/file1ac4238424941.xlsx': Sheet1
v Column names cleaned with janitor::clean_names().
v Successfully read sheet 1 from '/tmp/RtmpmL9GWn/working_dir/RtmpyQLugc/file1ac4238424941.xlsx'.
-- Reading Excel file --
i Sheets in '/tmp/RtmpmL9GWn/working_dir/RtmpyQLugc/file1ac423767bc71a.xlsx': Sheet1
v Successfully read sheet 1 from '/tmp/RtmpmL9GWn/working_dir/RtmpyQLugc/file1ac423767bc71a.xlsx'.
-- Reading Excel file --
i Sheets in '/tmp/RtmpmL9GWn/working_dir/RtmpyQLugc/file1ac4232d7005b3.xlsx': Sheet1
v Column names cleaned with janitor::clean_names().
v Successfully read sheet 1 from '/tmp/RtmpmL9GWn/working_dir/RtmpyQLugc/file1ac4232d7005b3.xlsx'.
Path: '/tmp/RtmpmL9GWn/working_dir/RtmpyQLugc/file1ac423107a30cb.csv'
Separator: "," | Encoding: "UTF-8"
OpenMP version (_OPENMP) 201511
omp_get_num_procs() 24
R_DATATABLE_NUM_PROCS_PERCENT unset (default 50)
R_DATATABLE_NUM_THREADS unset
R_DATATABLE_THROTTLE unset (default 1024)
omp_get_thread_limit() 2
omp_get_max_threads() 24
OMP_THREAD_LIMIT 2
OMP_NUM_THREADS unset
RestoreAfterFork true
data.table is using 2 threads with throttle==1024. See ?setDTthreads.
freadR.c has been passed a filename: /tmp/RtmpmL9GWn/working_dir/RtmpyQLugc/file1ac423107a30cb.csv
[01] Check arguments
Using 2 threads (omp_get_max_threads()=24, nth=2)
NAstrings = [<<NA>>]
None of the NAstrings look like numbers.
show progress = 1
0/1 column will be read as integer
Y/N column will be read as character
[02] Opening the file
Opening file /tmp/RtmpmL9GWn/working_dir/RtmpyQLugc/file1ac423107a30cb.csv
File opened, size = 235 bytes.
Memory mapped ok
[03] Detect and skip BOM
[04] Arrange mmap to be \0 terminated
\n has been found in the input (counts: 0 \r by themselves vs 6 [\r]*\n) and different lines can end with different line endings (e.g. mixed \n and \r\n in one file). This is common and ideal.
[05] Skipping initial rows if needed
Positioned on line 1 starting: <<mpg,cyl,disp,hp,drat,wt,qsec,v>>
[06] Detect separator, quoting rule, and ncolumns
Using supplied sep ','
sep=',' with 6 lines of 11 fields using quote rule 0
Detected 11 columns on line 1. This line is either column names or first data row. Line starts as: <<mpg,cyl,disp,hp,drat,wt,qsec,v>>
Quote rule picked = 0
fill=false and the most number of columns found is 11
[07] Detect column types, dec, good nrow estimate and whether first row is column names
'header' changed by user from 'auto' to true
sep=',' so dec set to '.'
Number of sampling jump points = 1 because (234 bytes from row 1 to eof) / (2 * 234 jump0size) == 0
Type codes (jump 000) : 97779997777 Quote rule 0
All rows were sampled since file is small so we know nrow=5 exactly
[08] Assign column names
[09] Apply user overrides on column types
After 0 type and 0 drop user overrides : 97779997777
[10] Allocate memory for the datatable
Allocating 11 column slots (11 - 0 dropped) with 5 rows
[11] Read the data
jumps=[0..1), chunk_size=1048576, total_size=189
Read 5 rows x 11 columns from 235 bytes file in 00:00.000 wall clock time
[12] Finalizing the datatable
Type counts:
7 : int32 '7'
4 : float64 '9'
=============================
0.000s ( 40%) Memory map 0.000GiB file
0.000s ( 41%) sep=',' ncol=11 and header detection
0.000s ( 5%) Column type detection using 5 sample rows
0.000s ( 4%) Allocation of 5 rows x 11 cols (0.000GiB) of which 5 (100%) rows used
0.000s ( 10%) Reading 1 chunks (0 swept) of 1.000MiB (each chunk 5 rows) using 1 threads
+ 0.000s ( 2%) Parse to row-major thread buffers (grown 0 times)
+ 0.000s ( 0%) Transpose
+ 0.000s ( 8%) Waiting
0.000s ( 0%) Rereading 0 columns due to out-of-sample type exceptions
0.000s Total
v File loaded successfully (5 rows \u00d7 11 cols)
-- glimpse
`glimpse(df)` from dplyr/tibble gives a compact overview.
-- glimpse
`glimpse(df)` from dplyr/tibble gives a compact overview.
-- read_excel
`readxl::read_excel("yourfile.xlsx")` reads Excel files. Supports `sheet =`, `range =`, etc.
-- glimpse
`glimpse(df)` from dplyr/tibble gives a compact overview.
-- Usage Examples --------------------------------------------------------------
-- glimpse
`glimpse(df)` from dplyr/tibble gives a compact overview.
-- read_excel
`readxl::read_excel("yourfile.xlsx")` reads Excel files. Supports `sheet =`, `range =`, etc.
-- droplevels
`droplevels(df)` removes unused factor levels from a data frame or factor.
-- modifyList
`modifyList(x, y)` merges two lists; elements in `y` overwrite those in `x`.
-- do.call
`do.call(fun, args)` calls a function with arguments in a list: `do.call(plot, list(x = 1:10))`.
-- sprintf
`sprintf("Hello, %s!", name)` formats strings with `%s`, `%d`, etc.
-- scRNAseq
`scRNAseq` (Bioconductor) provides scRNA-seq datasets, e.g., `ZeiselBrainData()`.
-- basename
`basename(path)` extracts the filename from a full path. See also `dirname()`.
-- here
`here::here("data", "raw", "sample1.rds")` builds a path from project root.
-- stopifnot
`stopifnot(cond1, cond2, ...)` throws if any condition is FALSE.
-- object.size
`object.size(x)` estimates memory size; use `format()` to pretty-print.
-- slice
`slice(df, 1:3)` selects rows by position; see `slice_head()`, `slice_tail()`, `slice_max()`.
-- unzip
`unzip("file.zip", exdir = "dir")` extracts ZIP archives.
-- gunzip
`R.utils::gunzip("file.csv.gz", remove = FALSE)` decompresses .gz files.
-- untar
`untar("file.tar.gz", exdir = "dir")` extracts .tar or .tar.gz archives.
-- NoLegend
`NoLegend()` removes legends from ggplot2/Seurat plots.
-- RotatedAxis
`RotatedAxis()` rotates x-axis text for readability in dot plots.
-- guides
`guides(fill = "none")` customizes or removes legends (with `scale_*`).
-- log2
`log2(x)` base-2 logarithm (often for fold change).
-- log
`log(x, base = exp(1))` natural log by default; set `base = 10` or `2` for others.
-- log10
`log10(x)` base-10 logarithm (orders of magnitude).
-- round
`round(x, digits = 0)` rounds; use `signif()` for significant digits.
-- floor
`floor(x)` greatest integer ≤ x (e.g., `floor(2.8)` -> 2).
-- ceiling
`ceiling(x)` smallest integer ≥ x (e.g., `ceiling(2.1)` -> 3).
-- cut
`cut(x, breaks)` bins numeric vector; `breaks = 3` or custom; `labels = FALSE` for group indices.
-- cumsum
`cumsum(x)` cumulative sum.
-- cumprod
`cumprod(x)` cumulative product.
-- cummin
`cummin(x)` running minimum.
-- cummax
`cummax(x)` running maximum.
-- row_number
`row_number(x)` order rank (ties broken arbitrarily).
-- min_rank
`min_rank(x)` ties get the same minimum rank.
-- dense_rank
`dense_rank(x)` like `min_rank()` but without gaps.
-- percent_rank
`percent_rank(x)` relative rank in [0,1], normalized by n-1.
-- cume_dist
`cume_dist(x)` cumulative proportion of values ≤ x.
-- str_view
`stringr::str_view(string, pattern)` highlights regex matches; `str_view_all()` for all.
-- str_c
`stringr::str_c(...)` concatenates; use `sep`/`collapse` as needed.
-- str_glue
`glue::glue("Hello, {name}!")` inline expressions with `{}`.
-- str_flatten
`stringr::str_flatten(x, collapse = ", ")` join a character vector.
-- str_length
`stringr::str_length(x)` string lengths.
-- str_sub
`stringr::str_sub(x, start, end)` extract/replace substrings (supports negative indices).
-- today
`lubridate::today()` current Date (no time).
-- now
`lubridate::now()` current POSIXct date-time.
-- Sys.timezone
`Sys.timezone()` system time zone name.
-- skimr
`skimr::skim(df)` compact, readable data summaries.
-- par
`par(mfrow = c(m, n))` split plotting area (e.g., 2x2).
-- layout
`layout(matrix, widths, heights)` flexible plot arrangement.
-- datatable
`DT::datatable(data)` interactive table (search/filter/sort/paginate).
-- windowsFonts
`windowsFonts()` register system fonts (Windows).
-- sign
`sign(x)` returns -1/0/1 for negative/zero/positive.
-- reactable
`reactable::reactable(data)` modern interactive table.
-- trimws
`trimws(x)` removes leading and trailing whitespace.
-- Available Keywords ----------------------------------------------------------
`glimpse, read_excel, droplevels, modifyList, do.call, sprintf, scRNAseq,
basename, here, stopifnot, object.size, slice, unzip, gunzip, untar, NoLegend,
RotatedAxis, guides, log2, log, log10, round, floor, ceiling, cut, cumsum,
cumprod, cummin, cummax, row_number, min_rank, dense_rank, percent_rank,
cume_dist, str_view, str_c, str_glue, str_flatten, str_length, str_sub, today,
now, Sys.timezone, skimr, par, layout, datatable, windowsFonts, sign,
reactable, trimws`
x No match found for keyword: "notakeyword"
-- min_rank
`min_rank(x)` ties get the same minimum rank.
-- dense_rank
`dense_rank(x)` like `min_rank()` but without gaps.
-- percent_rank
`percent_rank(x)` relative rank in [0,1], normalized by n-1.
v Palette removed from qualitative: '/tmp/RtmpmL9GWn/working_dir/RtmpyQLugc/palettes_test_1ac4231bd3d535/qualitative/test_palette.json'
! Palette not found in any type: nonexistent
v Palette removed from diverging: '/tmp/RtmpmL9GWn/working_dir/RtmpyQLugc/palettes_test_1ac4237d828c33/diverging/test_palette.json'
v Palette removed from qualitative: '/tmp/RtmpmL9GWn/working_dir/RtmpyQLugc/custom_palettes_1ac42359041021/qualitative/custom_test.json'
v RGB: c(255, 128, 0) → HEX: #FF8000
v RGB: c(0, 0, 0) → HEX: #000000
v RGB: c(255, 255, 255) → HEX: #FFFFFF
v Converted 3 RGB values to HEX.
i RGB: c(255, 128, 0) → HEX: #FF8000
i RGB: c(0, 255, 0) → HEX: #00FF00
i RGB: c(0, 0, 255) → HEX: #0000FF
v RGB: c(0, 1, 255) → HEX: #0001FF
x An error occurred: non-numeric argument to mathematical function
-- Setting cran mirror --
v CRAN mirror set to: <https://mirrors.tuna.tsinghua.edu.cn/CRAN>
i Available CRAN mirrors: "official", "rstudio", "tuna", "ustc", "aliyun", "sjtu", "pku", "hku", "westlake", "nju", and "sustech"
i View current settings: `getOption('repos')` & `getOption('BioC_mirror')`
-- Setting cran mirror --
v CRAN mirror set to: <https://mirrors.ustc.edu.cn/CRAN>
i Available CRAN mirrors: "official", "rstudio", "tuna", "ustc", "aliyun", "sjtu", "pku", "hku", "westlake", "nju", and "sustech"
i View current settings: `getOption('repos')` & `getOption('BioC_mirror')`
-- Setting cran mirror --
v CRAN mirror set to: <https://mirrors.westlake.edu.cn/CRAN>
i Available CRAN mirrors: "official", "rstudio", "tuna", "ustc", "aliyun", "sjtu", "pku", "hku", "westlake", "nju", and "sustech"
i View current settings: `getOption('repos')` & `getOption('BioC_mirror')`
-- Setting bioc mirror --
v Bioconductor mirror set to: <https://mirrors.tuna.tsinghua.edu.cn/bioconductor>
i Available Bioc mirrors: "official", "tuna", "ustc", "westlake", and "nju"
i View current settings: `getOption('repos')` & `getOption('BioC_mirror')`
-- Setting bioc mirror --
v Bioconductor mirror set to: <https://mirrors.ustc.edu.cn/bioconductor>
i Available Bioc mirrors: "official", "tuna", "ustc", "westlake", and "nju"
i View current settings: `getOption('repos')` & `getOption('BioC_mirror')`
-- Setting bioc mirror --
v Bioconductor mirror set to: <https://mirrors.westlake.edu.cn/bioconductor>
i Available Bioc mirrors: "official", "tuna", "ustc", "westlake", and "nju"
i View current settings: `getOption('repos')` & `getOption('BioC_mirror')`
-- Setting all mirror --
v CRAN mirror set to: <https://mirrors.tuna.tsinghua.edu.cn/CRAN>
v Bioconductor mirror set to: <https://mirrors.tuna.tsinghua.edu.cn/bioconductor>
i Available CRAN mirrors: "official", "rstudio", "tuna", "ustc", "aliyun", "sjtu", "pku", "hku", "westlake", "nju", and "sustech"
i Available Bioc mirrors: "official", "tuna", "ustc", "westlake", and "nju"
i View current settings: `getOption('repos')` & `getOption('BioC_mirror')`
-- Setting all mirror --
v CRAN mirror set to: <https://mirrors.ustc.edu.cn/CRAN>
v Bioconductor mirror set to: <https://mirrors.ustc.edu.cn/bioconductor>
i Available CRAN mirrors: "official", "rstudio", "tuna", "ustc", "aliyun", "sjtu", "pku", "hku", "westlake", "nju", and "sustech"
i Available Bioc mirrors: "official", "tuna", "ustc", "westlake", and "nju"
i View current settings: `getOption('repos')` & `getOption('BioC_mirror')`
-- Setting cran mirror --
-- Setting bioc mirror --
-- Setting cran mirror --
v CRAN mirror set to: <https://mirrors.tuna.tsinghua.edu.cn/CRAN>
i Available CRAN mirrors: "official", "rstudio", "tuna", "ustc", "aliyun", "sjtu", "pku", "hku", "westlake", "nju", and "sustech"
i View current settings: `getOption('repos')` & `getOption('BioC_mirror')`
-- Setting all mirror --
v CRAN mirror set to: <https://mirrors.tuna.tsinghua.edu.cn/CRAN>
v Bioconductor mirror set to: <https://mirrors.tuna.tsinghua.edu.cn/bioconductor>
i Available CRAN mirrors: "official", "rstudio", "tuna", "ustc", "aliyun", "sjtu", "pku", "hku", "westlake", "nju", and "sustech"
i Available Bioc mirrors: "official", "tuna", "ustc", "westlake", and "nju"
i View current settings: `getOption('repos')` & `getOption('BioC_mirror')`
-- Setting cran mirror --
i Available CRAN mirrors: "official", "rstudio", "tuna", "ustc", "aliyun", "sjtu", "pku", "hku", "westlake", "nju", and "sustech"
i View current settings: `getOption('repos')` & `getOption('BioC_mirror')`
-- Setting bioc mirror --
i Available Bioc mirrors: "official", "tuna", "ustc", "westlake", and "nju"
i View current settings: `getOption('repos')` & `getOption('BioC_mirror')`
-- Setting cran mirror --
v CRAN mirror set to: <https://mirrors.tuna.tsinghua.edu.cn/CRAN>
i View current settings: `getOption('repos')` & `getOption('BioC_mirror')`
-- Setting cran mirror --
v CRAN mirror set to: <https://mirrors.tuna.tsinghua.edu.cn/CRAN>
i Available CRAN mirrors: "official", "rstudio", "tuna", "ustc", "aliyun", "sjtu", "pku", "hku", "westlake", "nju", and "sustech"
-- Setting cran mirror --
v CRAN mirror set to: <https://mirrors.tuna.tsinghua.edu.cn/CRAN>
i Available CRAN mirrors: "official", "rstudio", "tuna", "ustc", "aliyun", "sjtu", "pku", "hku", "westlake", "nju", and "sustech"
i View current settings: `getOption('repos')` & `getOption('BioC_mirror')`
-- Setting bioc mirror --
-- Setting all mirror --
-- Setting cran mirror --
v CRAN mirror set to: <https://cloud.r-project.org>
i Available CRAN mirrors: "official", "rstudio", "tuna", "ustc", "aliyun", "sjtu", "pku", "hku", "westlake", "nju", and "sustech"
i View current settings: `getOption('repos')` & `getOption('BioC_mirror')`
-- Setting bioc mirror --
v Bioconductor mirror set to: <https://bioconductor.org>
i Available Bioc mirrors: "official", "tuna", "ustc", "westlake", and "nju"
i View current settings: `getOption('repos')` & `getOption('BioC_mirror')`
i Square test started at 2026-02-03 12:04:47
v Square test completed in 0.001 seconds
i Silent task started at 2026-02-03 12:04:47
v Silent task completed in 0.001 seconds
v Excel file written to '/tmp/RtmpmL9GWn/working_dir/RtmpyQLugc/file1ac4236516daf5.xlsx'
v Excel file written to '/tmp/RtmpmL9GWn/working_dir/RtmpyQLugc/file1ac423336b14f3.xlsx'
v Excel file written to '/tmp/RtmpmL9GWn/working_dir/RtmpyQLugc/file1ac423533704ee.xlsx'
! File already exists and will be overwritten: '/tmp/RtmpmL9GWn/working_dir/RtmpyQLugc/file1ac423533704ee.xlsx'
v Excel file written to '/tmp/RtmpmL9GWn/working_dir/RtmpyQLugc/file1ac423533704ee.xlsx'
v Excel file written to '/tmp/RtmpmL9GWn/working_dir/RtmpyQLugc/test-write-1ac42336a2276_2026-02-03.xlsx'
[ FAIL 8 | WARN 5 | SKIP 44 | PASS 1310 ]
══ Skipped tests (44) ══════════════════════════════════════════════════════════
• On CRAN (44): 'test-check_pkg.R:48:3', 'test-download_batch.R:19:3',
'test-download_batch.R:39:3', 'test-download_gene_ref.R:20:3',
'test-download_gene_ref.R:31:3', 'test-download_gene_ref.R:42:3',
'test-download_gene_ref.R:55:3', 'test-download_geo_data.R:11:3',
'test-download_geo_data.R:21:3', 'test-download_geo_data.R:50:3',
'test-download_geo_data.R:61:3', 'test-download_geo_data.R:80:3',
'test-download_geo_data.R:101:3', 'test-download_geo_data.R:155:3',
'test-download_geo_data.R:178:3', 'test-download_geo_data.R:208:3',
'test-download_url.R:10:3', 'test-download_url.R:22:3',
'test-download_url.R:39:3', 'test-download_url.R:103:3',
'test-download_url.R:117:3', 'test-download_url.R:147:3',
'test-download_url.R:177:3', 'test-download_url.R:205:3',
'test-download_url.R:227:3', 'test-download_url.R:252:3',
'test-download_url.R:279:3', 'test-download_url.R:306:3',
'test-file_info.R:12:3', 'test-file_info.R:26:3', 'test-file_info.R:48:3',
'test-file_info.R:59:3', 'test-file_info.R:71:3', 'test-pkg_version.R:19:3',
'test-pkg_version.R:27:3', 'test-pkg_version.R:37:3',
'test-pkg_version.R:48:3', 'test-plot_forest.R:11:3',
'test-plot_forest.R:32:3', 'test-plot_forest.R:53:3',
'test-plot_forest.R:71:3', 'test-plot_forest.R:93:3',
'test-plot_forest.R:119:3', 'test-plot_forest.R:140:3'
══ Failed tests ════════════════════════════════════════════════════════════════
── Failure ('test-plot_pie.R:69:3'): plot_pie() works with character vector input ──
Expected `p <- plot_pie(vec, preview = FALSE)` to run silently.
Actual noise: warnings.
── Failure ('test-plot_pie.R:75:3'): plot_pie() works with data.frame input ────
Expected `p <- plot_pie(df, group_col = "group", count_col = "count", preview = FALSE)` to run silently.
Actual noise: warnings.
── Failure ('test-plot_pie.R:97:5'): plot_pie() handles different label types ──
Expected `p <- plot_pie(df, label = lbl, preview = FALSE)` to run silently.
Actual noise: warnings.
── Failure ('test-plot_pie.R:97:5'): plot_pie() handles different label types ──
Expected `p <- plot_pie(df, label = lbl, preview = FALSE)` to run silently.
Actual noise: warnings.
── Failure ('test-plot_pie.R:97:5'): plot_pie() handles different label types ──
Expected `p <- plot_pie(df, label = lbl, preview = FALSE)` to run silently.
Actual noise: warnings.
── Failure ('test-plot_pie.R:97:5'): plot_pie() handles different label types ──
Expected `p <- plot_pie(df, label = lbl, preview = FALSE)` to run silently.
Actual noise: warnings.
── Failure ('test-plot_pie.R:135:3'): plot_pie() handles custom colors ─────────
Expected `p <- plot_pie(df, fill = custom_colors, preview = FALSE)` to run silently.
Actual noise: warnings.
── Failure ('test-plot_pie.R:141:3'): plot_pie() handles custom title and colors ──
Expected `... <- NULL` to run silently.
Actual noise: warnings.
[ FAIL 8 | WARN 5 | SKIP 44 | PASS 1310 ]
Error:
! Test failures.
Execution halted
Flavor: r-devel-linux-x86_64-fedora-gcc