Henning Redestig
| Snapshot Date: 2020-10-16 14:40:19 -0400 (Fri, 16 Oct 2020) |
| URL: https://git.bioconductor.org/packages/pcaMethods |
| Branch: RELEASE_3_11 |
| Last Commit: b839238 |
| Last Changed Date: 2020-04-27 14:14:06 -0400 (Mon, 27 Apr 2020) |
| Back to Multiple platform build/check report for BioC 3.11 |
|
This page was generated on 2020-10-17 11:57:22 -0400 (Sat, 17 Oct 2020).
| TO THE DEVELOPERS/MAINTAINERS OF THE pcaMethods PACKAGE: Please make sure to use the following settings in order to reproduce any error or warning you see on this page. |
| Package 1282/1905 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
| pcaMethods 1.80.0 Henning Redestig
| malbec2 | Linux (Ubuntu 18.04.4 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: pcaMethods |
| Version: 1.80.0 |
| Command: C:\Users\biocbuild\bbs-3.11-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:pcaMethods.install-out.txt --library=C:\Users\biocbuild\bbs-3.11-bioc\R\library --no-vignettes --timings pcaMethods_1.80.0.tar.gz |
| StartedAt: 2020-10-17 06:47:14 -0400 (Sat, 17 Oct 2020) |
| EndedAt: 2020-10-17 06:52:25 -0400 (Sat, 17 Oct 2020) |
| EllapsedTime: 311.3 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: pcaMethods.Rcheck |
| Warnings: 0 |
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### Running command:
###
### C:\Users\biocbuild\bbs-3.11-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:pcaMethods.install-out.txt --library=C:\Users\biocbuild\bbs-3.11-bioc\R\library --no-vignettes --timings pcaMethods_1.80.0.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.11-bioc/meat/pcaMethods.Rcheck'
* using R version 4.0.3 (2020-10-10)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'pcaMethods/DESCRIPTION' ... OK
* this is package 'pcaMethods' version '1.80.0'
* package encoding: UTF-8
* 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 'pcaMethods' 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
BPCA_initmodel: no visible global function definition for 'cov'
Q2: no visible global function definition for 'txtProgressBar'
Q2: no visible global function definition for 'setTxtProgressBar'
Q2: no visible global function definition for 'cor'
RnipalsPca: no visible global function definition for 'na.omit'
cvseg : <anonymous>: no visible global function definition for
'na.omit'
llsImpute: no visible global function definition for 'cor'
nlpca: no visible global function definition for 'runif'
nlpca: no visible global function definition for 'rnorm'
plot.pcaRes: no visible global function definition for 'gray'
plot.pcaRes: no visible global function definition for 'barplot'
plot.pcaRes: no visible global function definition for 'legend'
plotPcs : panel: no visible global function definition for 'abline'
plotPcs : panel: no visible global function definition for 'lines'
plotPcs : panel: no visible global function definition for 'points'
plotPcs : panel: no visible global function definition for 'text'
plotPcs: no visible global function definition for 'pairs'
ppca: no visible global function definition for 'rnorm'
ppca: no visible global function definition for 'cov'
robustSvd: no visible binding for global variable 'median'
simpleEllipse: no visible global function definition for 'qf'
svdImpute: no visible global function definition for 'prcomp'
svdPca: no visible global function definition for 'prcomp'
plot,pcaRes: no visible global function definition for 'gray'
plot,pcaRes: no visible global function definition for 'barplot'
plot,pcaRes: no visible global function definition for 'legend'
slplot,pcaRes: no visible global function definition for 'par'
slplot,pcaRes: no visible global function definition for 'layout'
slplot,pcaRes: no visible global function definition for 'abline'
slplot,pcaRes: no visible global function definition for 'lines'
Undefined global functions or variables:
abline barplot cor cov gray layout legend lines median na.omit pairs
par points prcomp qf rnorm runif setTxtProgressBar text
txtProgressBar
Consider adding
importFrom("grDevices", "gray")
importFrom("graphics", "abline", "barplot", "layout", "legend",
"lines", "pairs", "par", "points", "text")
importFrom("stats", "cor", "cov", "median", "na.omit", "prcomp", "qf",
"rnorm", "runif")
importFrom("utils", "setTxtProgressBar", "txtProgressBar")
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 line endings in C/C++/Fortran sources/headers ... OK
* checking compiled code ... NOTE
Note: information on .o files for i386 is not available
Note: information on .o files for x64 is not available
File 'C:/Users/biocbuild/bbs-3.11-bioc/R/library/pcaMethods/libs/i386/pcaMethods.dll':
Found 'abort', possibly from 'abort' (C), 'runtime' (Fortran)
Found 'exit', possibly from 'exit' (C), 'stop' (Fortran)
Found 'printf', possibly from 'printf' (C)
File 'C:/Users/biocbuild/bbs-3.11-bioc/R/library/pcaMethods/libs/x64/pcaMethods.dll':
Found 'abort', possibly from 'abort' (C), 'runtime' (Fortran)
Found 'exit', possibly from 'exit' (C), 'stop' (Fortran)
Found 'printf', possibly from 'printf' (C)
Compiled code should not call entry points which might terminate R nor
write to stdout/stderr instead of to the console, nor use Fortran I/O
nor system RNGs. The detected symbols are linked into the code but
might come from libraries and not actually be called.
See 'Writing portable packages' in the 'Writing R Extensions' manual.
* 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
kEstimate 66.30 0.24 66.87
robustSvd 18.59 0.00 18.60
robustPca 7.57 0.00 7.56
** running examples for arch 'x64' ... OK
Examples with CPU (user + system) or elapsed time > 5s
user system elapsed
kEstimate 67.56 0.11 67.73
robustSvd 16.88 0.03 16.90
robustPca 6.57 0.00 6.60
* 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: 2 NOTEs
See
'C:/Users/biocbuild/bbs-3.11-bioc/meat/pcaMethods.Rcheck/00check.log'
for details.
pcaMethods.Rcheck/00install.out
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###
### Running command:
###
### C:\cygwin\bin\curl.exe -O https://malbec2.bioconductor.org/BBS/3.11/bioc/src/contrib/pcaMethods_1.80.0.tar.gz && rm -rf pcaMethods.buildbin-libdir && mkdir pcaMethods.buildbin-libdir && C:\Users\biocbuild\bbs-3.11-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=pcaMethods.buildbin-libdir pcaMethods_1.80.0.tar.gz && C:\Users\biocbuild\bbs-3.11-bioc\R\bin\R.exe CMD INSTALL pcaMethods_1.80.0.zip && rm pcaMethods_1.80.0.tar.gz pcaMethods_1.80.0.zip
###
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% Total % Received % Xferd Average Speed Time Time Time Current
Dload Upload Total Spent Left Speed
0 0 0 0 0 0 0 0 --:--:-- --:--:-- --:--:-- 0
100 172k 100 172k 0 0 2192k 0 --:--:-- --:--:-- --:--:-- 2395k
install for i386
* installing *source* package 'pcaMethods' ...
** using staged installation
** libs
"C:/rtools40/mingw32/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.11-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/Rcpp/include' -I"C:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c RcppExports.cpp -o RcppExports.o
"C:/rtools40/mingw32/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.11-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/Rcpp/include' -I"C:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c nipals.cpp -o nipals.o
C:/rtools40/mingw32/bin/g++ -std=gnu++11 -shared -s -static-libgcc -o pcaMethods.dll tmp.def RcppExports.o nipals.o -LC:/extsoft/lib/i386 -LC:/extsoft/lib -LC:/Users/BIOCBU~1/BBS-3~1.11-/R/bin/i386 -lR
installing to C:/Users/biocbuild/bbs-3.11-bioc/meat/pcaMethods.buildbin-libdir/00LOCK-pcaMethods/00new/pcaMethods/libs/i386
** R
** data
** inst
** byte-compile and prepare package for lazy loading
Creating a new generic function for 'loadings' in package 'pcaMethods'
** help
*** installing help indices
converting help for package 'pcaMethods'
finding HTML links ... done
BPCA_dostep html
BPCA_initmodel html
DModX-pcaRes-method html
Q2 html
R2VX-pcaRes-method html
R2cum-pcaRes-method html
RnipalsPca html
asExprSet html
biplot-methods html
bpca html
center-pcaRes-method html
centered-pcaRes-method html
checkData html
completeObs-nniRes-method html
cvseg html
cvstat-pcaRes-method html
deletediagonals html
derrorHierarchic html
dim.pcaRes html
errorHierarchic html
fitted-methods html
forkNlpcaNet html
getHierarchicIdx html
helix html
kEstimate html
kEstimateFast html
leverage-pcaRes-method html
lineSearch html
linr html
listPcaMethods html
llsImpute html
loadings-ANY-method html
loadings-pcaRes-method html
loadings.pcaRes html
metaboliteData html
metaboliteDataComplete html
method-pcaRes-method html
nObs-pcaRes-method html
nP-pcaRes-method html
nPcs-pcaRes-method html
nVar-pcaRes-method html
nipalsPca html
nlpca html
nmissing-pcaRes-method html
nni html
nniRes html
optiAlgCgd html
orth html
pca html
pcaMethods-deprecated html
pcaMethods html
pcaNet html
pcaRes html
plot.pcaRes html
plotPcs html
ppca html
predict-methods html
prep html
rediduals-methods html
repmat html
robustPca html
robustSvd html
sDev-pcaRes-method html
scaled-pcaRes-method html
scl-pcaRes-method html
scores-pcaRes-method html
scores.pcaRes html
show-methods html
showNniRes html
simpleEllipse html
slplot-pcaRes-method html
sortFeatures html
summary html
svdImpute html
svdPca html
tempFixNas html
vector2matrices-matrix-method html
vector2matrices-nlpcaNet-method html
wasna-pcaRes-method html
weightsAccount html
** building package indices
** installing vignettes
** 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 'pcaMethods' ...
** libs
"C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.11-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/Rcpp/include' -I"C:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c RcppExports.cpp -o RcppExports.o
"C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.11-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/Rcpp/include' -I"C:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c nipals.cpp -o nipals.o
C:/rtools40/mingw64/bin/g++ -std=gnu++11 -shared -s -static-libgcc -o pcaMethods.dll tmp.def RcppExports.o nipals.o -LC:/extsoft/lib/x64 -LC:/extsoft/lib -LC:/Users/BIOCBU~1/BBS-3~1.11-/R/bin/x64 -lR
installing to C:/Users/biocbuild/bbs-3.11-bioc/meat/pcaMethods.buildbin-libdir/pcaMethods/libs/x64
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'pcaMethods' as pcaMethods_1.80.0.zip
* DONE (pcaMethods)
* installing to library 'C:/Users/biocbuild/bbs-3.11-bioc/R/library'
package 'pcaMethods' successfully unpacked and MD5 sums checked
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pcaMethods.Rcheck/examples_i386/pcaMethods-Ex.timings
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pcaMethods.Rcheck/examples_x64/pcaMethods-Ex.timings
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