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CHECK report for maigesPack on malbec1

This page was generated on 2019-04-16 11:48:28 -0400 (Tue, 16 Apr 2019).

Package 868/1649HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
maigesPack 1.46.0
Gustavo H. Esteves
Snapshot Date: 2019-04-15 17:01:12 -0400 (Mon, 15 Apr 2019)
URL: https://git.bioconductor.org/packages/maigesPack
Branch: RELEASE_3_8
Last Commit: 36d093a
Last Changed Date: 2018-10-30 11:41:44 -0400 (Tue, 30 Oct 2018)
malbec1 Linux (Ubuntu 16.04.6 LTS) / x86_64  OK  OK [ OK ]UNNEEDED, same version exists in internal repository
merida1 OS X 10.11.6 El Capitan / x86_64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: maigesPack
Version: 1.46.0
Command: /home/biocbuild/bbs-3.8-bioc/R/bin/R CMD check --install=check:maigesPack.install-out.txt --library=/home/biocbuild/bbs-3.8-bioc/R/library --no-vignettes --timings maigesPack_1.46.0.tar.gz
StartedAt: 2019-04-16 01:06:05 -0400 (Tue, 16 Apr 2019)
EndedAt: 2019-04-16 01:07:55 -0400 (Tue, 16 Apr 2019)
EllapsedTime: 109.3 seconds
RetCode: 0
Status:  OK 
CheckDir: maigesPack.Rcheck
Warnings: 0

Command output

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### Running command:
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###   /home/biocbuild/bbs-3.8-bioc/R/bin/R CMD check --install=check:maigesPack.install-out.txt --library=/home/biocbuild/bbs-3.8-bioc/R/library --no-vignettes --timings maigesPack_1.46.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.8-bioc/meat/maigesPack.Rcheck’
* using R version 3.5.3 (2019-03-11)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘maigesPack/DESCRIPTION’ ... OK
* this is package ‘maigesPack’ version ‘1.46.0’
* 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 for sufficient/correct file permissions ... OK
* checking whether package ‘maigesPack’ can be installed ... OK
* 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
* 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 is not available
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU or elapsed time > 5s
                user system elapsed
plot-methods   6.536  0.424   7.596
normScaleLimma 6.548  0.316   6.880
* 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: 5 NOTEs
See
  ‘/home/biocbuild/bbs-3.8-bioc/meat/maigesPack.Rcheck/00check.log’
for details.



Installation output

maigesPack.Rcheck/00install.out

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### Running command:
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###   /home/biocbuild/bbs-3.8-bioc/R/bin/R CMD INSTALL maigesPack
###
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* installing to library ‘/home/biocbuild/bbs-3.8-bioc/R/library’
* installing *source* package ‘maigesPack’ ...
** libs
gcc -I"/home/biocbuild/bbs-3.8-bioc/R/include" -DNDEBUG   -I/usr/local/include   -fpic  -g -O2  -Wall -c Minfo.c -o Minfo.o
gcc -I"/home/biocbuild/bbs-3.8-bioc/R/include" -DNDEBUG   -I/usr/local/include   -fpic  -g -O2  -Wall -c bootstrapT.c -o bootstrapT.o
gcc -I"/home/biocbuild/bbs-3.8-bioc/R/include" -DNDEBUG   -I/usr/local/include   -fpic  -g -O2  -Wall -c register.c -o register.o
gcc -I"/home/biocbuild/bbs-3.8-bioc/R/include" -DNDEBUG   -I/usr/local/include   -fpic  -g -O2  -Wall -c robustCorr.c -o robustCorr.o
gcc -I"/home/biocbuild/bbs-3.8-bioc/R/include" -DNDEBUG   -I/usr/local/include   -fpic  -g -O2  -Wall -c stats.c -o stats.o
gcc -shared -L/home/biocbuild/bbs-3.8-bioc/R/lib -L/usr/local/lib -o maigesPack.so Minfo.o bootstrapT.o register.o robustCorr.o stats.o -L/home/biocbuild/bbs-3.8-bioc/R/lib -lR
installing to /home/biocbuild/bbs-3.8-bioc/R/library/maigesPack/libs
** R
** data
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (maigesPack)

Tests output


Example timings

maigesPack.Rcheck/maigesPack-Ex.timings

nameusersystemelapsed
MI0.0000.0000.002
activeMod1.3520.0441.418
activeModScoreHTML0.5120.0320.548
activeNet2.4920.0282.526
activeNetScoreHTML2.6080.0322.653
addGeneGrps000
addPaths000
bootstrapCor0.0320.0000.033
bootstrapMI0.1520.0080.161
bootstrapT0.0040.0000.003
boxplot-methods1.7760.1961.987
bracketMethods0.1280.0160.146
calcA0.1200.0560.174
calcW0.1240.0560.181
classifyKNN0.2360.0560.314
classifyKNNsc0.3480.0440.404
classifyLDA0.6280.0680.712
classifyLDAsc1.1520.0601.233
classifySVM0.440.040.50
classifySVMsc0.6960.1000.811
coerce-methods0.0920.0120.105
compCorr000
createMaigesRaw0.1920.0200.219
deGenes2by2BootT0.4040.0480.458
deGenes2by2Ttest0.2720.0720.352
deGenes2by2Wilcox0.2320.0440.282
deGenesANOVA0.1720.0960.286
designANOVA0.1360.0360.179
dim-methods0.0960.0000.097
getLabels0.0880.0000.086
hierM1.2560.0121.211
hierMde1.6440.1241.781
image-methods1.3200.0641.403
kmeansM1.1280.0361.176
kmeansMde0.3800.0280.419
loadData000
normLoc1.9640.1122.097
normOLIN0.0600.0000.064
normRepLoess0.0640.0000.065
normScaleLimma6.5480.3166.880
normScaleMarray1.2600.1961.467
plot-methods6.5360.4247.596
plotGenePair0.1120.0400.156
print-methods0.1800.0160.195
relNet2TGF0.1600.0720.246
relNetworkB1.7120.1681.902
relNetworkM0.1360.0680.212
robustCorr0.0000.0000.001
selSpots0.3040.1440.470
show-methods0.1760.0120.187
somM1.7280.0361.772
somMde0.4960.0800.587
summarizeReplicates0.9960.1201.145
summary-methods0.1480.0080.157
tableClass0.760.080.85
tablesDE3.1200.2043.342