Gustavo H. Esteves
| Snapshot Date: 2020-10-16 14:40:19 -0400 (Fri, 16 Oct 2020) |
| URL: https://git.bioconductor.org/packages/maigesPack |
| Branch: RELEASE_3_11 |
| Last Commit: 6be25be |
| Last Changed Date: 2020-04-27 14:15:57 -0400 (Mon, 27 Apr 2020) |
| Back to Multiple platform build/check report for BioC 3.11 |
|
This page was generated on 2020-10-17 11:56:59 -0400 (Sat, 17 Oct 2020).
| TO THE DEVELOPERS/MAINTAINERS OF THE maigesPack PACKAGE: Please make sure to use the following settings in order to reproduce any error or warning you see on this page. |
| Package 977/1905 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
| maigesPack 1.52.0 Gustavo H. Esteves
| malbec2 | Linux (Ubuntu 18.04.4 LTS) / x86_64 | OK | OK | OK | | ||||||
| tokay2 | Windows Server 2012 R2 Standard / x64 | OK | OK | [ WARNINGS ] | OK | | ||||||
| machv2 | macOS 10.14.6 Mojave / x86_64 | OK | OK | OK | OK | |
| Package: maigesPack |
| Version: 1.52.0 |
| Command: C:\Users\biocbuild\bbs-3.11-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:maigesPack.install-out.txt --library=C:\Users\biocbuild\bbs-3.11-bioc\R\library --no-vignettes --timings maigesPack_1.52.0.tar.gz |
| StartedAt: 2020-10-17 05:37:35 -0400 (Sat, 17 Oct 2020) |
| EndedAt: 2020-10-17 05:41:17 -0400 (Sat, 17 Oct 2020) |
| EllapsedTime: 222.5 seconds |
| RetCode: 0 |
| Status: WARNINGS |
| CheckDir: maigesPack.Rcheck |
| Warnings: 1 |
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### Running command:
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### C:\Users\biocbuild\bbs-3.11-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:maigesPack.install-out.txt --library=C:\Users\biocbuild\bbs-3.11-bioc\R\library --no-vignettes --timings maigesPack_1.52.0.tar.gz
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* using log directory 'C:/Users/biocbuild/bbs-3.11-bioc/meat/maigesPack.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 'maigesPack/DESCRIPTION' ... OK
* this is package 'maigesPack' version '1.52.0'
* 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 ... NOTE
Found the following hidden files and directories:
.BBSoptions
These were most likely included in error. See section 'Package
structure' in the 'Writing R Extensions' manual.
* checking for portable file names ... OK
* checking whether package 'maigesPack' can be installed ... WARNING
Found the following significant warnings:
Rd warning: C:/Users/biocbuild/bbs-3.11-bioc/tmpdir/Rtmpyi7EJI/R.INSTALL1af4415b2e8f/maigesPack/man/plot-methods.Rd:19: file link 'plot' in package 'graphics' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.11-bioc/tmpdir/Rtmpyi7EJI/R.INSTALL1af4415b2e8f/maigesPack/man/plot-methods.Rd:83: file link 'plot' in package 'graphics' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.11-bioc/tmpdir/Rtmpyi7EJI/R.INSTALL1af4415b2e8f/maigesPack/man/plot-methods.Rd:198: file link 'plot' in package 'graphics' does not exist and so has been treated as a topic
See 'C:/Users/biocbuild/bbs-3.11-bioc/meat/maigesPack.Rcheck/00install.out' for details.
* checking installed package size ... OK
* checking package directory ... OK
* checking 'build' directory ... OK
* checking DESCRIPTION meta-information ... NOTE
Malformed Description field: should contain one or more complete sentences.
* 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 ... NOTE
'library' or 'require' calls in package code:
'OLIN' 'annotate' 'rgl'
Please use :: or requireNamespace() instead.
See section 'Suggested packages' in the 'Writing R Extensions' manual.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
activeMod: no visible global function definition for 'sessionInfo'
activeModScoreHTML: no visible binding for global variable 'data'
activeNet: no visible global function definition for 'sessionInfo'
activeNetScoreHTML: no visible binding for global variable 'data'
blackBlue: no visible global function definition for 'col2rgb'
blackBlue: no visible global function definition for 'rgb'
classifyKNN: no visible global function definition for 'sessionInfo'
classifyKNNsc: no visible global function definition for 'sessionInfo'
classifyLDA: no visible global function definition for 'sessionInfo'
classifyLDAsc: no visible global function definition for 'sessionInfo'
classifySVM: no visible global function definition for 'sessionInfo'
classifySVMsc: no visible global function definition for 'sessionInfo'
createMaigesRaw: no visible global function definition for
'sessionInfo'
createTDMS: no visible global function definition for 'write.table'
deGenes2by2BootT: no visible global function definition for
'sessionInfo'
deGenes2by2Ttest: no visible global function definition for
'sessionInfo'
deGenes2by2Wilcox: no visible global function definition for
'sessionInfo'
deGenesANOVA: no visible global function definition for 'sessionInfo'
designANOVA: no visible global function definition for 'sessionInfo'
greenRed: no visible global function definition for 'col2rgb'
greenRed: no visible global function definition for 'rgb'
loadData: no visible global function definition for 'read.table'
loadData: no visible global function definition for 'sessionInfo'
normLoc: no visible global function definition for 'sessionInfo'
normOLIN: no visible global function definition for 'sessionInfo'
normRepLoess: no visible global function definition for 'sessionInfo'
normScaleLimma: no visible global function definition for 'sessionInfo'
normScaleMarray: no visible global function definition for
'sessionInfo'
print.maiges: no visible global function definition for 'str'
print.maigesANOVA: no visible global function definition for 'str'
print.maigesPreRaw: no visible global function definition for 'str'
print.maigesRaw: no visible global function definition for 'str'
relNet2TGF.maigesRelNetB: no visible global function definition for
'write.table'
relNet2TGF.maigesRelNetM: no visible global function definition for
'write.table'
relNetworkB: no visible global function definition for 'sessionInfo'
relNetworkM: no visible global function definition for 'sessionInfo'
selSpots: no visible global function definition for 'sessionInfo'
summarizeReplicates: no visible global function definition for
'sessionInfo'
tableClass: no visible global function definition for 'write.table'
tablesDE: no visible global function definition for 'setRepository'
tablesDE: no visible global function definition for 'write.table'
Undefined global functions or variables:
col2rgb data read.table rgb sessionInfo setRepository str write.table
Consider adding
importFrom("grDevices", "col2rgb", "rgb")
importFrom("utils", "data", "read.table", "sessionInfo", "str",
"write.table")
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/maigesPack/libs/i386/maigesPack.dll':
Found 'abort', possibly from 'abort' (C), 'runtime' (Fortran)
File 'C:/Users/biocbuild/bbs-3.11-bioc/R/library/maigesPack/libs/x64/maigesPack.dll':
Found 'abort', possibly from 'abort' (C), 'runtime' (Fortran)
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
normScaleLimma 7.86 0.80 8.66
plot-methods 5.44 0.09 5.93
** running examples for arch 'x64' ... OK
Examples with CPU (user + system) or elapsed time > 5s
user system elapsed
normScaleLimma 8.76 1.11 9.87
plot-methods 6.80 0.09 6.97
* 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 WARNING, 5 NOTEs
See
'C:/Users/biocbuild/bbs-3.11-bioc/meat/maigesPack.Rcheck/00check.log'
for details.
maigesPack.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/maigesPack_1.52.0.tar.gz && rm -rf maigesPack.buildbin-libdir && mkdir maigesPack.buildbin-libdir && C:\Users\biocbuild\bbs-3.11-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=maigesPack.buildbin-libdir maigesPack_1.52.0.tar.gz && C:\Users\biocbuild\bbs-3.11-bioc\R\bin\R.exe CMD INSTALL maigesPack_1.52.0.zip && rm maigesPack_1.52.0.tar.gz maigesPack_1.52.0.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 854k 100 854k 0 0 5742k 0 --:--:-- --:--:-- --:--:-- 6015k
install for i386
* installing *source* package 'maigesPack' ...
** using staged installation
** libs
"C:/rtools40/mingw32/bin/"gcc -I"C:/Users/BIOCBU~1/BBS-3~1.11-/R/include" -DNDEBUG -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c Minfo.c -o Minfo.o
"C:/rtools40/mingw32/bin/"gcc -I"C:/Users/BIOCBU~1/BBS-3~1.11-/R/include" -DNDEBUG -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c bootstrapT.c -o bootstrapT.o
"C:/rtools40/mingw32/bin/"gcc -I"C:/Users/BIOCBU~1/BBS-3~1.11-/R/include" -DNDEBUG -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c register.c -o register.o
"C:/rtools40/mingw32/bin/"gcc -I"C:/Users/BIOCBU~1/BBS-3~1.11-/R/include" -DNDEBUG -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c robustCorr.c -o robustCorr.o
"C:/rtools40/mingw32/bin/"gcc -I"C:/Users/BIOCBU~1/BBS-3~1.11-/R/include" -DNDEBUG -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c stats.c -o stats.o
C:/rtools40/mingw32/bin/gcc -shared -s -static-libgcc -o maigesPack.dll tmp.def Minfo.o bootstrapT.o register.o robustCorr.o stats.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/maigesPack.buildbin-libdir/00LOCK-maigesPack/00new/maigesPack/libs/i386
** R
** data
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
converting help for package 'maigesPack'
finding HTML links ... done
MI html
activeMod html
activeModScoreHTML html
activeNet html
activeNetScoreHTML html
addGeneGrps html
addPaths html
bootstrapCor html
bootstrapMI html
bootstrapT html
boxplot-methods html
bracketMethods html
calcA html
calcW html
classifyKNN html
classifyKNNsc html
classifyLDA html
classifyLDAsc html
classifySVM html
classifySVMsc html
coerce-methods html
compCorr html
contrastsFitM html
createMaigesRaw html
createTDMS html
deGenes2by2BootT html
deGenes2by2Ttest html
deGenes2by2Wilcox html
deGenesANOVA html
designANOVA html
dim-methods html
gastro html
getLabels html
heatmapsM html
hierM html
hierMde html
image-methods html
kmeansM html
kmeansMde html
loadData html
maiges-class html
maigesANOVA-class html
maigesActMod-class html
maigesActNet-class html
maigesClass-class html
maigesDE-class html
maigesDEcluster-class html
maigesPreRaw-class html
maigesRaw-class html
maigesRelNetB-class html
maigesRelNetM-class html
normLoc html
normOLIN html
normRepLoess html
normScaleLimma html
normScaleMarray html
plot-methods html
Rd warning: C:/Users/biocbuild/bbs-3.11-bioc/tmpdir/Rtmpyi7EJI/R.INSTALL1af4415b2e8f/maigesPack/man/plot-methods.Rd:19: file link 'plot' in package 'graphics' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.11-bioc/tmpdir/Rtmpyi7EJI/R.INSTALL1af4415b2e8f/maigesPack/man/plot-methods.Rd:83: file link 'plot' in package 'graphics' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.11-bioc/tmpdir/Rtmpyi7EJI/R.INSTALL1af4415b2e8f/maigesPack/man/plot-methods.Rd:198: file link 'plot' in package 'graphics' does not exist and so has been treated as a topic
plotGenePair html
print-methods html
relNet2TGF html
relNetworkB html
relNetworkM html
robustCorr html
selSpots html
show-methods html
somM html
somMde html
summarizeReplicates html
summary-methods html
tableClass html
tablesDE 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 'maigesPack' ...
** libs
"C:/rtools40/mingw64/bin/"gcc -I"C:/Users/BIOCBU~1/BBS-3~1.11-/R/include" -DNDEBUG -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c Minfo.c -o Minfo.o
"C:/rtools40/mingw64/bin/"gcc -I"C:/Users/BIOCBU~1/BBS-3~1.11-/R/include" -DNDEBUG -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c bootstrapT.c -o bootstrapT.o
"C:/rtools40/mingw64/bin/"gcc -I"C:/Users/BIOCBU~1/BBS-3~1.11-/R/include" -DNDEBUG -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c register.c -o register.o
"C:/rtools40/mingw64/bin/"gcc -I"C:/Users/BIOCBU~1/BBS-3~1.11-/R/include" -DNDEBUG -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c robustCorr.c -o robustCorr.o
"C:/rtools40/mingw64/bin/"gcc -I"C:/Users/BIOCBU~1/BBS-3~1.11-/R/include" -DNDEBUG -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c stats.c -o stats.o
C:/rtools40/mingw64/bin/gcc -shared -s -static-libgcc -o maigesPack.dll tmp.def Minfo.o bootstrapT.o register.o robustCorr.o stats.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/maigesPack.buildbin-libdir/maigesPack/libs/x64
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'maigesPack' as maigesPack_1.52.0.zip
* DONE (maigesPack)
* installing to library 'C:/Users/biocbuild/bbs-3.11-bioc/R/library'
package 'maigesPack' successfully unpacked and MD5 sums checked
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maigesPack.Rcheck/examples_i386/maigesPack-Ex.timings
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maigesPack.Rcheck/examples_x64/maigesPack-Ex.timings
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