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This page was generated on 2021-10-21 12:04:22 -0400 (Thu, 21 Oct 2021).

CHECK results for maigesPack on nebbiolo2

To the developers/maintainers of the maigesPack package:
- Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/maigesPack.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.

raw results

Package 1034/2075HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
maigesPack 1.57.0  (landing page)
Gustavo H. Esteves
Snapshot Date: 2021-10-20 14:50:05 -0400 (Wed, 20 Oct 2021)
git_url: https://git.bioconductor.org/packages/maigesPack
git_branch: master
git_last_commit: 9eda04e
git_last_commit_date: 2021-05-19 11:39:47 -0400 (Wed, 19 May 2021)
nebbiolo2Linux (Ubuntu 20.04.2 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
riesling1Windows Server 2019 Standard / x64  OK    OK    OK    OK  UNNEEDED, same version is already published
merida1macOS 10.14.6 Mojave / x86_64  OK    OK    OK    NA  

Summary

Package: maigesPack
Version: 1.57.0
Command: /home/biocbuild/bbs-3.14-bioc/R/bin/R CMD check --install=check:maigesPack.install-out.txt --library=/home/biocbuild/bbs-3.14-bioc/R/library --no-vignettes --timings maigesPack_1.57.0.tar.gz
StartedAt: 2021-10-20 20:50:12 -0400 (Wed, 20 Oct 2021)
EndedAt: 2021-10-20 20:51:52 -0400 (Wed, 20 Oct 2021)
EllapsedTime: 100.1 seconds
RetCode: 0
Status:   OK  
CheckDir: maigesPack.Rcheck
Warnings: 0

Command output

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### Running command:
###
###   /home/biocbuild/bbs-3.14-bioc/R/bin/R CMD check --install=check:maigesPack.install-out.txt --library=/home/biocbuild/bbs-3.14-bioc/R/library --no-vignettes --timings maigesPack_1.57.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.14-bioc/meat/maigesPack.Rcheck’
* using R version 4.1.1 (2021-08-10)
* 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 ‘1.57.0’
* 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 (user + system) or elapsed time > 5s
                user system elapsed
normScaleLimma 5.112  0.208   5.320
plot-methods   4.789  0.118   5.001
* 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-3.14-bioc/meat/maigesPack.Rcheck/00check.log’
for details.



Installation output

maigesPack.Rcheck/00install.out

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###
### Running command:
###
###   /home/biocbuild/bbs-3.14-bioc/R/bin/R CMD INSTALL maigesPack
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.14-bioc/R/library’
* installing *source* package ‘maigesPack’ ...
** using staged installation
** libs
gcc -I"/home/biocbuild/bbs-3.14-bioc/R/include" -DNDEBUG   -I/usr/local/include   -fpic  -g -O2  -Wall -c Minfo.c -o Minfo.o
gcc -I"/home/biocbuild/bbs-3.14-bioc/R/include" -DNDEBUG   -I/usr/local/include   -fpic  -g -O2  -Wall -c bootstrapT.c -o bootstrapT.o
gcc -I"/home/biocbuild/bbs-3.14-bioc/R/include" -DNDEBUG   -I/usr/local/include   -fpic  -g -O2  -Wall -c register.c -o register.o
gcc -I"/home/biocbuild/bbs-3.14-bioc/R/include" -DNDEBUG   -I/usr/local/include   -fpic  -g -O2  -Wall -c robustCorr.c -o robustCorr.o
gcc -I"/home/biocbuild/bbs-3.14-bioc/R/include" -DNDEBUG   -I/usr/local/include   -fpic  -g -O2  -Wall -c stats.c -o stats.o
gcc -shared -L/home/biocbuild/bbs-3.14-bioc/R/lib -L/usr/local/lib -o maigesPack.so Minfo.o bootstrapT.o register.o robustCorr.o stats.o -L/home/biocbuild/bbs-3.14-bioc/R/lib -lR
installing to /home/biocbuild/bbs-3.14-bioc/R/library/00LOCK-maigesPack/00new/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 from temporary location
** checking absolute paths in shared objects and dynamic libraries
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (maigesPack)

Tests output


Example timings

maigesPack.Rcheck/maigesPack-Ex.timings

nameusersystemelapsed
MI0.0020.0000.003
activeMod1.0770.0521.129
activeModScoreHTML0.4520.0080.460
activeNet2.3380.0442.382
activeNetScoreHTML2.1910.0082.199
addGeneGrps000
addPaths000
bootstrapCor0.0260.0000.026
bootstrapMI0.140.000.14
bootstrapT0.0020.0000.002
boxplot-methods2.4580.3082.766
bracketMethods0.1470.0040.151
calcA0.0990.0680.166
calcW0.1060.0640.170
classifyKNN0.1720.0040.175
classifyKNNsc0.2180.0120.230
classifyLDA0.5280.0080.536
classifyLDAsc1.0330.0041.041
classifySVM0.4510.0000.451
classifySVMsc0.5960.0040.600
coerce-methods0.0860.0120.098
compCorr0.0010.0000.001
createMaigesRaw0.1750.0040.179
deGenes2by2BootT0.3050.0000.305
deGenes2by2Ttest0.1670.0040.171
deGenes2by2Wilcox0.1850.0040.189
deGenesANOVA0.1340.0040.138
designANOVA0.0960.0040.101
dim-methods0.0640.0040.068
getLabels0.0590.0120.071
hierM1.3930.0081.264
hierMde1.4280.0281.455
image-methods1.1870.0191.207
kmeansM1.1060.0361.107
kmeansMde0.2430.0030.245
loadData000
normLoc0.8770.0000.877
normOLIN0.0630.0000.063
normRepLoess0.0630.0000.064
normScaleLimma5.1120.2085.320
normScaleMarray1.3370.0241.361
plot-methods4.7890.1185.001
plotGenePair0.0920.0160.107
print-methods0.1100.0080.118
relNet2TGF0.1050.0120.116
relNetworkB1.1590.0241.183
relNetworkM0.0860.0040.090
robustCorr000
selSpots0.1770.0040.181
show-methods0.1030.0080.111
somM0.9620.0120.951
somMde0.2360.0120.247
summarizeReplicates1.0080.0241.032
summary-methods0.1130.0080.121
tableClass0.4630.0160.479
tablesDE3.9550.1364.091