Back to Multiple platform build/check report for BioC 3.16
ABCDEFGHIJKL[M]NOPQRSTUVWXYZ

This page was generated on 2022-06-24 11:06:42 -0400 (Fri, 24 Jun 2022).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 20.04.4 LTS)x86_644.2.0 Patched (2022-06-02 r82447) -- "Vigorous Calisthenics" 4331
palomino4Windows Server 2022 Datacenterx644.2.0 Patched (2022-06-02 r82447 ucrt) -- "Vigorous Calisthenics" 4136
lconwaymacOS 12.2.1 Montereyx86_644.2.0 Patched (2022-05-29 r82424) -- "Vigorous Calisthenics" 4147
Click on any hostname to see more info about the system (e.g. compilers)      (*) as reported by 'uname -p', except on Windows and Mac OS X

CHECK results for maigesPack on palomino4


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? 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 1053/2118HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
maigesPack 1.61.0  (landing page)
Gustavo H. Esteves
Snapshot Date: 2022-06-23 14:00:04 -0400 (Thu, 23 Jun 2022)
git_url: https://git.bioconductor.org/packages/maigesPack
git_branch: master
git_last_commit: f3e5688
git_last_commit_date: 2022-04-26 11:00:27 -0400 (Tue, 26 Apr 2022)
nebbiolo2Linux (Ubuntu 20.04.4 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
palomino4Windows Server 2022 Datacenter / x64  OK    OK    OK    OK  UNNEEDED, same version is already published
lconwaymacOS 12.2.1 Monterey / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published

Summary

Package: maigesPack
Version: 1.61.0
Command: F:\biocbuild\bbs-3.16-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:maigesPack.install-out.txt --library=F:\biocbuild\bbs-3.16-bioc\R\library --no-vignettes --timings maigesPack_1.61.0.tar.gz
StartedAt: 2022-06-24 02:59:09 -0400 (Fri, 24 Jun 2022)
EndedAt: 2022-06-24 03:01:08 -0400 (Fri, 24 Jun 2022)
EllapsedTime: 118.7 seconds
RetCode: 0
Status:   OK  
CheckDir: maigesPack.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   F:\biocbuild\bbs-3.16-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:maigesPack.install-out.txt --library=F:\biocbuild\bbs-3.16-bioc\R\library --no-vignettes --timings maigesPack_1.61.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'F:/biocbuild/bbs-3.16-bioc/meat/maigesPack.Rcheck'
* using R version 4.2.0 Patched (2022-06-02 r82447 ucrt)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: UTF-8
* using option '--no-vignettes'
* checking for file 'maigesPack/DESCRIPTION' ... OK
* this is package 'maigesPack' version '1.61.0'
* 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 ... 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 for x64 is not available
File 'F:/biocbuild/bbs-3.16-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 sizes of PDF files under 'inst/doc' ... OK
* checking files in 'vignettes' ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
               user system elapsed
normScaleLimma 6.65   0.73    7.39
plot-methods   5.12   0.17    5.31
* 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
  'F:/biocbuild/bbs-3.16-bioc/meat/maigesPack.Rcheck/00check.log'
for details.



Installation output

maigesPack.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O http://155.52.207.166/BBS/3.16/bioc/src/contrib/maigesPack_1.61.0.tar.gz && rm -rf maigesPack.buildbin-libdir && mkdir maigesPack.buildbin-libdir && F:\biocbuild\bbs-3.16-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=maigesPack.buildbin-libdir maigesPack_1.61.0.tar.gz && F:\biocbuild\bbs-3.16-bioc\R\bin\R.exe CMD INSTALL maigesPack_1.61.0.zip && rm maigesPack_1.61.0.tar.gz maigesPack_1.61.0.zip
###
##############################################################################
##############################################################################


  % 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  860k  100  860k    0     0  7606k      0 --:--:-- --:--:-- --:--:-- 7678k
only one architecture so ignoring '--merge-multiarch'
* installing *source* package 'maigesPack' ...
** using staged installation
** libs
gcc  -I"F:/biocbuild/bbs-3.16-bioc/R/include" -DNDEBUG     -I"C:/rtools42/x86_64-w64-mingw32.static.posix/include"     -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign  -c Minfo.c -o Minfo.o
gcc  -I"F:/biocbuild/bbs-3.16-bioc/R/include" -DNDEBUG     -I"C:/rtools42/x86_64-w64-mingw32.static.posix/include"     -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign  -c bootstrapT.c -o bootstrapT.o
gcc  -I"F:/biocbuild/bbs-3.16-bioc/R/include" -DNDEBUG     -I"C:/rtools42/x86_64-w64-mingw32.static.posix/include"     -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign  -c register.c -o register.o
gcc  -I"F:/biocbuild/bbs-3.16-bioc/R/include" -DNDEBUG     -I"C:/rtools42/x86_64-w64-mingw32.static.posix/include"     -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign  -c robustCorr.c -o robustCorr.o
gcc  -I"F:/biocbuild/bbs-3.16-bioc/R/include" -DNDEBUG     -I"C:/rtools42/x86_64-w64-mingw32.static.posix/include"     -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign  -c stats.c -o stats.o
gcc -shared -s -static-libgcc -o maigesPack.dll tmp.def Minfo.o bootstrapT.o register.o robustCorr.o stats.o -LC:/rtools42/x86_64-w64-mingw32.static.posix/lib/x64 -LC:/rtools42/x86_64-w64-mingw32.static.posix/lib -LF:/biocbuild/bbs-3.16-bioc/R/bin/x64 -lR
installing to F:/biocbuild/bbs-3.16-bioc/meat/maigesPack.buildbin-libdir/00LOCK-maigesPack/00new/maigesPack/libs/x64
** 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
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* MD5 sums
packaged installation of 'maigesPack' as maigesPack_1.61.0.zip
* DONE (maigesPack)
* installing to library 'F:/biocbuild/bbs-3.16-bioc/R/library'
package 'maigesPack' successfully unpacked and MD5 sums checked

Tests output


Example timings

maigesPack.Rcheck/maigesPack-Ex.timings

nameusersystemelapsed
MI000
activeMod1.240.061.29
activeModScoreHTML0.490.050.53
activeNet2.390.142.53
activeNetScoreHTML2.250.202.45
addGeneGrps000
addPaths000
bootstrapCor0.030.000.04
bootstrapMI0.120.000.12
bootstrapT000
boxplot-methods2.521.073.58
bracketMethods0.150.000.15
calcA0.200.070.28
calcW0.170.110.28
classifyKNN0.210.030.24
classifyKNNsc0.250.040.28
classifyLDA0.580.010.59
classifyLDAsc0.820.030.86
classifySVM0.320.050.36
classifySVMsc0.650.020.67
coerce-methods0.100.030.13
compCorr000
createMaigesRaw0.150.010.17
deGenes2by2BootT0.330.000.33
deGenes2by2Ttest0.140.030.17
deGenes2by2Wilcox0.160.000.16
deGenesANOVA0.090.030.12
designANOVA0.100.020.11
dim-methods0.060.000.06
getLabels0.060.020.08
hierM0.750.040.80
hierMde1.270.051.31
image-methods1.060.081.14
kmeansM0.830.080.92
kmeansMde0.220.000.22
loadData000
normLoc0.640.060.70
normOLIN0.060.000.07
normRepLoess0.050.000.04
normScaleLimma6.650.737.39
normScaleMarray1.30.31.6
plot-methods5.120.175.31
plotGenePair0.130.020.14
print-methods0.090.000.10
relNet2TGF0.110.040.14
relNetworkB1.160.021.17
relNetworkM0.080.020.10
robustCorr000
selSpots0.200.010.22
show-methods0.090.020.11
somM0.750.070.84
somMde0.280.020.30
summarizeReplicates1.100.031.12
summary-methods0.080.030.11
tableClass0.390.030.42
tablesDE3.620.113.74