Sonia Tarazona
| Snapshot Date: 2021-10-14 04:50:12 -0400 (Thu, 14 Oct 2021) |
| git_url: https://git.bioconductor.org/packages/NOISeq |
| git_branch: RELEASE_3_13 |
| git_last_commit: c6b5b95 |
| git_last_commit_date: 2021-05-19 11:54:29 -0400 (Wed, 19 May 2021) |
| Back to Multiple platform build/check report for BioC 3.13 |
|
This page was generated on 2021-10-15 15:06:14 -0400 (Fri, 15 Oct 2021).
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To the developers/maintainers of the NOISeq package: - Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/NOISeq.git to reflect on this report. See How and When does the builder pull? When will my changes propagate? here for more information. - Make sure to use the following settings in order to reproduce any error or warning you see on this page. |
| Package 1274/2041 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| NOISeq 2.36.0 (landing page) Sonia Tarazona
| nebbiolo1 | Linux (Ubuntu 20.04.2 LTS) / x86_64 | OK | OK | OK | | ||||||||
| tokay2 | Windows Server 2012 R2 Standard / x64 | OK | OK | OK | OK | | ||||||||
| machv2 | macOS 10.14.6 Mojave / x86_64 | OK | OK | OK | OK | | ||||||||
| Package: NOISeq |
| Version: 2.36.0 |
| Command: C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:NOISeq.install-out.txt --library=C:\Users\biocbuild\bbs-3.13-bioc\R\library --no-vignettes --timings NOISeq_2.36.0.tar.gz |
| StartedAt: 2021-10-15 02:46:06 -0400 (Fri, 15 Oct 2021) |
| EndedAt: 2021-10-15 02:48:45 -0400 (Fri, 15 Oct 2021) |
| EllapsedTime: 159.4 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: NOISeq.Rcheck |
| Warnings: 0 |
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### Running command:
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### C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:NOISeq.install-out.txt --library=C:\Users\biocbuild\bbs-3.13-bioc\R\library --no-vignettes --timings NOISeq_2.36.0.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.13-bioc/meat/NOISeq.Rcheck'
* using R version 4.1.1 (2021-08-10)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'NOISeq/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'NOISeq' version '2.36.0'
* checking package namespace information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for hidden files and directories ... OK
* checking for portable file names ... OK
* checking whether package 'NOISeq' can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking 'build' directory ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking R files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* loading checks for arch 'i386'
** checking whether the package can be loaded ... OK
** checking whether the package can be loaded with stated dependencies ... OK
** checking whether the package can be unloaded cleanly ... OK
** checking whether the namespace can be loaded with stated dependencies ... OK
** checking whether the namespace can be unloaded cleanly ... OK
* loading checks for arch 'x64'
** checking whether the package can be loaded ... OK
** checking whether the package can be loaded with stated dependencies ... OK
** checking whether the package can be unloaded cleanly ... OK
** checking whether the namespace can be loaded with stated dependencies ... OK
** checking whether the namespace can be unloaded cleanly ... OK
* checking dependencies in R code ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
.calcFactorQuantile : <anonymous>: no visible global function
definition for 'quantile'
CV: no visible global function definition for 'sd'
DE.plot: no visible global function definition for 'par'
DE.plot: no visible global function definition for 'points'
DE.plot: no visible global function definition for 'axis'
DE.plot: no visible global function definition for 'na.omit'
DE.plot: no visible global function definition for 'aggregate'
DE.plot: no visible global function definition for 'abline'
DE.plot: no visible global function definition for 'rect'
DE.plot: no visible global function definition for 'segments'
DE.plot: no visible global function definition for 'text'
DE.plot: no visible global function definition for 'layout'
DE.plot: no visible global function definition for 'barplot'
DE.plot: no visible global function definition for 'legend'
GC.dat: no visible global function definition for 'quantile'
GC.dat: no visible global function definition for 'aggregate'
GC.dat: no visible global function definition for 'lm'
GC.plot: no visible global function definition for 'par'
GC.plot: no visible global function definition for 'matplot'
GC.plot: no visible global function definition for 'text'
GC.plot: no visible global function definition for 'pf'
GC.plot: no visible global function definition for 'legend'
GC.plot: no visible global function definition for 'layout'
MD: no visible global function definition for 'combn'
MD.plot: no visible global function definition for 'quantile'
MD.plot: no visible global function definition for 'points'
MD.plot: no visible global function definition for 'legend'
MDbio: no visible global function definition for 'combn'
MDbio: no visible global function definition for 'quantile'
PCA.plot: no visible global function definition for 'colors'
PCA.plot: no visible global function definition for 'points'
PCA.plot: no visible global function definition for 'legend'
QCreport: no visible global function definition for 'pdf'
QCreport: no visible global function definition for 'layout'
QCreport: no visible global function definition for 'par'
QCreport: no visible global function definition for 'text'
QCreport: no visible global function definition for 'abline'
QCreport : <anonymous>: no visible global function definition for 'pf'
QCreport: no visible global function definition for 'dev.off'
allMDbio: no visible binding for global variable 'sd'
biodetection.plot: no visible global function definition for 'par'
biodetection.plot: no visible global function definition for 'barplot'
biodetection.plot: no visible global function definition for 'axis'
biodetection.plot: no visible global function definition for 'abline'
biodetection.plot: no visible global function definition for 'legend'
biodetection.plot: no visible global function definition for
'prop.test'
biodetection.plot: no visible global function definition for 'lines'
cd.dat : <anonymous>: no visible binding for global variable 'median'
cd.dat: no visible binding for global variable 'quantile'
cd.plot: no visible binding for global variable 'density'
cd.plot: no visible global function definition for 'abline'
cd.plot: no visible global function definition for 'median'
cd.plot: no visible global function definition for 'lines'
cd.plot: no visible global function definition for 'legend'
countsbio.plot: no visible global function definition for 'par'
countsbio.plot: no visible global function definition for 'barplot'
countsbio.plot: no visible global function definition for 'abline'
countsbio.plot: no visible global function definition for 'mtext'
countsbio.plot: no visible global function definition for 'legend'
countsbio.plot: no visible global function definition for 'boxplot'
countsbio.plot: no visible global function definition for 'axis'
degenes: no visible global function definition for 'na.omit'
filtered.data : <anonymous>: no visible global function definition for
'wilcox.test'
filtered.data: no visible global function definition for 'p.adjust'
filtered.data : <anonymous>: no visible global function definition for
'prop.test'
length.dat: no visible global function definition for 'quantile'
length.dat: no visible global function definition for 'aggregate'
length.dat: no visible global function definition for 'lm'
length.plot: no visible global function definition for 'par'
length.plot: no visible global function definition for 'matplot'
length.plot: no visible global function definition for 'text'
length.plot: no visible global function definition for 'pf'
length.plot: no visible global function definition for 'legend'
length.plot: no visible global function definition for 'layout'
noiseqbio: no visible global function definition for 'density'
noiseqbio: no visible global function definition for 'approxfun'
noiseqbio: no visible global function definition for 'lines'
noiseqbio: no visible global function definition for 'legend'
plot.y2: no visible global function definition for 'axis'
plot.y2: no visible global function definition for 'points'
plot.y2: no visible global function definition for 'lines'
plot.y2: no visible global function definition for 'supsmu'
plot.y2: no visible global function definition for 'mtext'
plot.y2: no visible global function definition for 'par'
plot.y2: no visible global function definition for 'box'
probdeg: no visible global function definition for 'na.omit'
rpkm: no visible global function definition for 'na.omit'
saturation.dat: no visible global function definition for 'rmultinom'
saturation.plot: no visible global function definition for 'par'
saturation.plot: no visible global function definition for 'colors'
saturation.plot: no visible global function definition for 'lines'
saturation.plot: no visible global function definition for 'points'
saturation.plot: no visible global function definition for 'na.omit'
saturation.plot: no visible global function definition for 'layout'
saturation.plot: no visible global function definition for 'rect'
saturation.plot: no visible global function definition for 'text'
share.info: no visible global function definition for 'kmeans'
share.info : <anonymous>: no visible global function definition for
'sd'
share.info: no visible global function definition for 'quantile'
sim.samples: no visible global function definition for 'runif'
sim.samples: no visible global function definition for 'rmultinom'
tmm: no visible global function definition for 'na.omit'
uqua: no visible binding for global variable 'quantile'
uqua: no visible global function definition for 'na.omit'
Undefined global functions or variables:
abline aggregate approxfun axis barplot box boxplot colors combn
density dev.off kmeans layout legend lines lm matplot median mtext
na.omit p.adjust par pdf pf points prop.test quantile rect rmultinom
runif sd segments supsmu text wilcox.test
Consider adding
importFrom("grDevices", "colors", "dev.off", "pdf")
importFrom("graphics", "abline", "axis", "barplot", "box", "boxplot",
"layout", "legend", "lines", "matplot", "mtext", "par",
"points", "rect", "segments", "text")
importFrom("stats", "aggregate", "approxfun", "density", "kmeans",
"lm", "median", "na.omit", "p.adjust", "pf", "prop.test",
"quantile", "rmultinom", "runif", "sd", "supsmu",
"wilcox.test")
importFrom("utils", "combn")
to your NAMESPACE file.
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking contents of 'data' directory ... OK
* checking data for non-ASCII characters ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking installed files from 'inst/doc' ... OK
* checking files in 'vignettes' ... OK
* checking examples ...
** running examples for arch 'i386' ... OK
Examples with CPU (user + system) or elapsed time > 5s
user system elapsed
noiseq 16.67 0.38 17.14
noiseqbio 8.02 0.05 8.09
QCreport 6.58 0.14 6.78
** running examples for arch 'x64' ... OK
Examples with CPU (user + system) or elapsed time > 5s
user system elapsed
noiseq 15.20 0.49 15.69
noiseqbio 8.24 0.05 8.28
QCreport 6.75 0.11 6.86
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in 'inst/doc' ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE
Status: 1 NOTE
See
'C:/Users/biocbuild/bbs-3.13-bioc/meat/NOISeq.Rcheck/00check.log'
for details.
NOISeq.Rcheck/00install.out
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###
### Running command:
###
### C:\cygwin\bin\curl.exe -O http://155.52.207.165/BBS/3.13/bioc/src/contrib/NOISeq_2.36.0.tar.gz && rm -rf NOISeq.buildbin-libdir && mkdir NOISeq.buildbin-libdir && C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=NOISeq.buildbin-libdir NOISeq_2.36.0.tar.gz && C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD INSTALL NOISeq_2.36.0.zip && rm NOISeq_2.36.0.tar.gz NOISeq_2.36.0.zip
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% Total % Received % Xferd Average Speed Time Time Time Current
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0 0 0 0 0 0 0 0 --:--:-- --:--:-- --:--:-- 0
100 757k 100 757k 0 0 2010k 0 --:--:-- --:--:-- --:--:-- 2015k
install for i386
* installing *source* package 'NOISeq' ...
** using staged installation
** R
** data
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
converting help for package 'NOISeq'
finding HTML links ... done
ARSyNSeq html
REDIRECT:topic Previous alias or file overwritten by alias: C:/Users/biocbuild/bbs-3.13-bioc/meat/NOISeq.buildbin-libdir/00LOCK-NOISeq/00new/NOISeq/help/arsynseq.html
Biodetection html
CD html
CountsBio html
DE.plot html
GCcontentBias html
LengthBias html
Marioni html
Output html
PCA.GENES html
PCA html
QCreport html
Saturation html
REDIRECT:topic Previous alias or file overwritten by alias: C:/Users/biocbuild/bbs-3.13-bioc/meat/NOISeq.buildbin-libdir/00LOCK-NOISeq/00new/NOISeq/help/saturation.html
dat html
dat2save html
degenes html
example html
explo.plot html
filter.low.counts html
myCounts html
REDIRECT:topic Previous alias or file overwritten by alias: C:/Users/biocbuild/bbs-3.13-bioc/meat/NOISeq.buildbin-libdir/00LOCK-NOISeq/00new/NOISeq/help/myCounts.html
noiseq html
noiseqbio html
normalization html
readData html
** building package indices
** installing vignettes
'NOISeq.Rnw' using 'UTF-8'
** testing if installed package can be loaded from temporary location
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
install for x64
* installing *source* package 'NOISeq' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'NOISeq' as NOISeq_2.36.0.zip
* DONE (NOISeq)
* installing to library 'C:/Users/biocbuild/bbs-3.13-bioc/R/library'
package 'NOISeq' successfully unpacked and MD5 sums checked
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NOISeq.Rcheck/examples_i386/NOISeq-Ex.timings
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NOISeq.Rcheck/examples_x64/NOISeq-Ex.timings
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