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BioC 3.4: CHECK report for maigesPack on moscato1

This page was generated on 2016-09-21 03:42:21 -0700 (Wed, 21 Sep 2016).

Package 681/1257HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
maigesPack 1.37.0
Gustavo H. Esteves
Snapshot Date: 2016-09-19 19:15:14 -0700 (Mon, 19 Sep 2016)
URL: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/maigesPack
Last Changed Rev: 117081 / Revision: 121152
Last Changed Date: 2016-05-03 14:30:44 -0700 (Tue, 03 May 2016)
zin1 Linux (Ubuntu 16.04 LTS) / x86_64  NotNeeded  OK  OK UNNEEDED, same version exists in internal repository
moscato1 Windows Server 2008 R2 Standard (64-bit) / x64  NotNeeded  OK [ OK ] OK UNNEEDED, same version exists in internal repository
morelia Mac OS X Mavericks (10.9.5) / x86_64  NotNeeded  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: maigesPack
Version: 1.37.0
Command: rm -rf maigesPack.buildbin-libdir maigesPack.Rcheck && mkdir maigesPack.buildbin-libdir maigesPack.Rcheck && D:\biocbld\bbs-3.4-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=maigesPack.buildbin-libdir maigesPack_1.37.0.tar.gz >maigesPack.Rcheck\00install.out 2>&1 && cp maigesPack.Rcheck\00install.out maigesPack-install.out && D:\biocbld\bbs-3.4-bioc\R\bin\R.exe CMD check --library=maigesPack.buildbin-libdir --install="check:maigesPack-install.out" --force-multiarch --no-vignettes --timings maigesPack_1.37.0.tar.gz
StartedAt: 2016-09-20 11:23:24 -0700 (Tue, 20 Sep 2016)
EndedAt: 2016-09-20 11:27:38 -0700 (Tue, 20 Sep 2016)
EllapsedTime: 253.9 seconds
RetCode: 0
Status:  OK  
CheckDir: maigesPack.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   rm -rf maigesPack.buildbin-libdir maigesPack.Rcheck && mkdir maigesPack.buildbin-libdir maigesPack.Rcheck && D:\biocbld\bbs-3.4-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=maigesPack.buildbin-libdir maigesPack_1.37.0.tar.gz >maigesPack.Rcheck\00install.out 2>&1 && cp maigesPack.Rcheck\00install.out maigesPack-install.out  && D:\biocbld\bbs-3.4-bioc\R\bin\R.exe CMD check --library=maigesPack.buildbin-libdir --install="check:maigesPack-install.out" --force-multiarch --no-vignettes --timings maigesPack_1.37.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'D:/biocbld/bbs-3.4-bioc/meat/maigesPack.Rcheck'
* using R version 3.3.1 (2016-06-21)
* 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 '1.37.0'
* 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
* 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
** checking loading without being on the library search path ... 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 loading without being on the library search path ... 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 'D:/biocbld/bbs-3.4-bioc/meat/maigesPack.buildbin-libdir/maigesPack/libs/i386/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 the system RNG.
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 installed files from 'inst/doc' ... OK
* checking files in 'vignettes' ... OK
* checking examples ...
** running examples for arch 'i386' ... OK
Examples with CPU or elapsed time > 5s
                 user system elapsed
normScaleLimma  15.68   0.62   16.94
plot-methods     6.53   0.09    6.68
boxplot-methods  4.37   0.79    5.16
** running examples for arch 'x64' ... OK
Examples with CPU or elapsed time > 5s
                    user system elapsed
normScaleLimma     14.39   0.67   15.10
plot-methods        8.58   0.03    9.20
activeNet           6.27   0.00    6.28
boxplot-methods     5.15   0.79    5.96
activeNetScoreHTML  5.27   0.01    5.30
* 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
  'D:/biocbld/bbs-3.4-bioc/meat/maigesPack.Rcheck/00check.log'
for details.


maigesPack.Rcheck/00install.out:


install for i386

* installing *source* package 'maigesPack' ...
** libs
C:/Rtools/mingw_32/bin/gcc  -I"D:/biocbld/BBS-3˜1.4-B/R/include" -DNDEBUG     -I"c:/local323/include"     -O3 -Wall  -std=gnu99 -mtune=core2 -c Minfo.c -o Minfo.o
C:/Rtools/mingw_32/bin/gcc  -I"D:/biocbld/BBS-3˜1.4-B/R/include" -DNDEBUG     -I"c:/local323/include"     -O3 -Wall  -std=gnu99 -mtune=core2 -c bootstrapT.c -o bootstrapT.o
C:/Rtools/mingw_32/bin/gcc  -I"D:/biocbld/BBS-3˜1.4-B/R/include" -DNDEBUG     -I"c:/local323/include"     -O3 -Wall  -std=gnu99 -mtune=core2 -c register.c -o register.o
C:/Rtools/mingw_32/bin/gcc  -I"D:/biocbld/BBS-3˜1.4-B/R/include" -DNDEBUG     -I"c:/local323/include"     -O3 -Wall  -std=gnu99 -mtune=core2 -c robustCorr.c -o robustCorr.o
C:/Rtools/mingw_32/bin/gcc  -I"D:/biocbld/BBS-3˜1.4-B/R/include" -DNDEBUG     -I"c:/local323/include"     -O3 -Wall  -std=gnu99 -mtune=core2 -c stats.c -o stats.o
C:/Rtools/mingw_32/bin/gcc -shared -s -static-libgcc -o maigesPack.dll tmp.def Minfo.o bootstrapT.o register.o robustCorr.o stats.o -Lc:/local323/lib/i386 -Lc:/local323/lib -LD:/biocbld/BBS-3˜1.4-B/R/bin/i386 -lR
installing to D:/biocbld/bbs-3.4-bioc/meat/maigesPack.buildbin-libdir/maigesPack/libs/i386
** R
** data
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded

install for x64

* installing *source* package 'maigesPack' ...
** libs
C:/Rtools/mingw_64/bin/gcc  -I"D:/biocbld/BBS-3˜1.4-B/R/include" -DNDEBUG     -I"c:/local323/include"     -O2 -Wall  -std=gnu99 -mtune=core2 -c Minfo.c -o Minfo.o
C:/Rtools/mingw_64/bin/gcc  -I"D:/biocbld/BBS-3˜1.4-B/R/include" -DNDEBUG     -I"c:/local323/include"     -O2 -Wall  -std=gnu99 -mtune=core2 -c bootstrapT.c -o bootstrapT.o
C:/Rtools/mingw_64/bin/gcc  -I"D:/biocbld/BBS-3˜1.4-B/R/include" -DNDEBUG     -I"c:/local323/include"     -O2 -Wall  -std=gnu99 -mtune=core2 -c register.c -o register.o
C:/Rtools/mingw_64/bin/gcc  -I"D:/biocbld/BBS-3˜1.4-B/R/include" -DNDEBUG     -I"c:/local323/include"     -O2 -Wall  -std=gnu99 -mtune=core2 -c robustCorr.c -o robustCorr.o
C:/Rtools/mingw_64/bin/gcc  -I"D:/biocbld/BBS-3˜1.4-B/R/include" -DNDEBUG     -I"c:/local323/include"     -O2 -Wall  -std=gnu99 -mtune=core2 -c stats.c -o stats.o
C:/Rtools/mingw_64/bin/gcc -shared -s -static-libgcc -o maigesPack.dll tmp.def Minfo.o bootstrapT.o register.o robustCorr.o stats.o -Lc:/local323/lib/x64 -Lc:/local323/lib -LD:/biocbld/BBS-3˜1.4-B/R/bin/x64 -lR
installing to D:/biocbld/bbs-3.4-bioc/meat/maigesPack.buildbin-libdir/maigesPack/libs/x64
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'maigesPack' as maigesPack_1.37.0.zip
* DONE (maigesPack)

maigesPack.Rcheck/examples_i386/maigesPack-Ex.timings:

nameusersystemelapsed
MI000
activeMod1.720.031.75
activeModScoreHTML0.940.001.03
activeNet3.710.003.71
activeNetScoreHTML3.600.003.61
addGeneGrps000
addPaths000
bootstrapCor0.030.000.03
bootstrapMI0.230.000.24
bootstrapT000
boxplot-methods4.370.795.16
bracketMethods0.170.000.17
calcA0.200.050.25
calcW0.220.050.27
classifyKNN0.200.000.21
classifyKNNsc0.250.010.26
classifyLDA0.630.020.64
classifyLDAsc1.130.001.14
classifySVM0.460.030.48
classifySVMsc0.670.000.67
coerce-methods0.110.000.11
compCorr000
createMaigesRaw0.210.000.22
deGenes2by2BootT0.640.000.64
deGenes2by2Ttest0.240.010.25
deGenes2by2Wilcox0.20.00.2
deGenesANOVA0.190.000.19
designANOVA0.110.000.11
dim-methods0.080.020.09
getLabels0.090.000.09
hierM1.280.011.33
hierMde1.170.031.20
image-methods1.430.001.44
kmeansM1.470.001.46
kmeansMde0.360.020.38
loadData000
normLoc1.230.001.23
normOLIN0.080.000.08
normRepLoess0.080.000.08
normScaleLimma15.68 0.6216.94
normScaleMarray2.370.412.77
plot-methods6.530.096.68
plotGenePair0.110.000.11
print-methods0.140.020.15
relNet2TGF0.220.010.23
relNetworkB1.740.021.76
relNetworkM0.110.000.11
robustCorr000
selSpots0.190.010.21
show-methods0.140.000.14
somM1.660.021.93
somMde0.370.000.38
summarizeReplicates1.280.021.29
summary-methods0.140.000.14
tableClass0.620.000.62
tablesDE2.610.042.66

maigesPack.Rcheck/examples_x64/maigesPack-Ex.timings:

nameusersystemelapsed
MI000
activeMod2.480.022.49
activeModScoreHTML1.160.031.20
activeNet6.270.006.28
activeNetScoreHTML5.270.015.30
addGeneGrps000
addPaths000
bootstrapCor0.060.000.07
bootstrapMI0.280.000.28
bootstrapT000
boxplot-methods5.150.795.96
bracketMethods0.170.000.17
calcA0.220.020.23
calcW0.190.060.25
classifyKNN0.200.020.22
classifyKNNsc0.360.010.38
classifyLDA0.750.020.76
classifyLDAsc1.360.011.37
classifySVM0.460.000.47
classifySVMsc0.780.020.80
coerce-methods0.110.000.11
compCorr000
createMaigesRaw0.240.000.23
deGenes2by2BootT0.510.020.53
deGenes2by2Ttest0.270.000.26
deGenes2by2Wilcox0.240.000.23
deGenesANOVA0.220.000.22
designANOVA0.100.000.11
dim-methods0.070.010.08
getLabels0.070.000.08
hierM1.440.051.48
hierMde1.310.051.36
image-methods1.500.011.51
kmeansM1.540.021.56
kmeansMde0.420.010.45
loadData000
normLoc1.290.001.31
normOLIN0.080.000.08
normRepLoess0.060.000.06
normScaleLimma14.39 0.6715.10
normScaleMarray2.810.333.14
plot-methods8.580.039.20
plotGenePair0.170.000.17
print-methods0.220.020.24
relNet2TGF0.210.000.21
relNetworkB2.130.032.16
relNetworkM0.090.010.11
robustCorr0.020.000.01
selSpots0.20.00.2
show-methods0.140.020.16
somM1.640.031.67
somMde0.400.030.44
summarizeReplicates1.810.031.84
summary-methods0.140.000.14
tableClass0.640.020.65
tablesDE3.450.033.92