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This page was generated on 2021-07-31 12:05:41 -0400 (Sat, 31 Jul 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 1009/2015HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
maigesPack 1.57.0  (landing page)
Gustavo H. Esteves
Snapshot Date: 2021-07-30 14:50:06 -0400 (Fri, 30 Jul 2021)
URL: https://git.bioconductor.org/packages/maigesPack
Branch: master
Last Commit: 9eda04e
Last Changed 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    OK  UNNEEDED, same version is already published

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: 2021-07-30 20:09:51 -0400 (Fri, 30 Jul 2021)
EndedAt: 2021-07-30 20:11:19 -0400 (Fri, 30 Jul 2021)
EllapsedTime: 88.4 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
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.14-bioc/meat/maigesPack.Rcheck’
* using R version 4.1.0 beta (2021-05-03 r80259)
* 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
* 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
MI0.0030.0000.003
activeMod0.9610.0200.981
activeModScoreHTML0.4210.0040.425
activeNet2.0680.0282.096
activeNetScoreHTML2.0430.1482.191
addGeneGrps000
addPaths0.0000.0000.001
bootstrapCor0.0250.0000.025
bootstrapMI0.1280.0000.128
bootstrapT0.0030.0000.002
boxplot-methods1.8390.2202.059
bracketMethods0.1290.0000.129
calcA0.1110.0480.158
calcW0.1240.0360.159
classifyKNN0.1460.0000.145
classifyKNNsc0.1920.0080.199
classifyLDA0.4720.0000.472
classifyLDAsc0.7770.0040.781
classifySVM0.3040.0080.311
classifySVMsc0.5320.0040.536
coerce-methods0.0760.0150.091
compCorr000
createMaigesRaw0.1580.0000.159
deGenes2by2BootT0.2790.0040.284
deGenes2by2Ttest0.1320.0080.141
deGenes2by2Wilcox0.1380.0040.141
deGenesANOVA0.1230.0000.123
designANOVA0.0850.0000.084
dim-methods0.0610.0000.060
getLabels0.0580.0080.065
hierM0.8290.0030.748
hierMde1.1940.0371.229
image-methods0.8980.0190.917
kmeansM0.8570.0440.864
kmeansMde0.2210.0000.220
loadData000
normLoc0.8320.0040.837
normOLIN0.0520.0080.060
normRepLoess0.0630.0000.063
normScaleLimma4.3430.1684.511
normScaleMarray0.9910.0080.999
plot-methods4.1990.1034.289
plotGenePair0.0960.0000.096
print-methods0.1060.0040.110
relNet2TGF0.1090.0040.114
relNetworkB1.0620.0361.098
relNetworkM0.0840.0080.092
robustCorr0.0000.0000.001
selSpots0.1710.0200.192
show-methods0.0980.0120.110
somM0.9800.0160.965
somMde0.2660.0040.268
summarizeReplicates0.9660.0280.994
summary-methods0.0920.0160.109
tableClass0.3790.0000.379
tablesDE3.2550.1603.415