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BioC 3.4: CHECK report for crlmm on moscato1

This page was generated on 2016-09-21 03:42:44 -0700 (Wed, 21 Sep 2016).

Package 272/1257HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
crlmm 1.31.2
Benilton S Carvalho , Robert Scharpf , Matt Ritchie
Snapshot Date: 2016-09-19 19:15:14 -0700 (Mon, 19 Sep 2016)
URL: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/crlmm
Last Changed Rev: 117175 / Revision: 121152
Last Changed Date: 2016-05-05 23:53:13 -0700 (Thu, 05 May 2016)
zin1 Linux (Ubuntu 16.04 LTS) / x86_64  OK  OK  WARNINGS UNNEEDED, same version exists in internal repository
moscato1 Windows Server 2008 R2 Standard (64-bit) / x64  OK  OK [ WARNINGS ] OK UNNEEDED, same version exists in internal repository
morelia Mac OS X Mavericks (10.9.5) / x86_64  OK  OK  WARNINGS  OK UNNEEDED, same version exists in internal repository

Summary

Package: crlmm
Version: 1.31.2
Command: rm -rf crlmm.buildbin-libdir crlmm.Rcheck && mkdir crlmm.buildbin-libdir crlmm.Rcheck && D:\biocbld\bbs-3.4-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=crlmm.buildbin-libdir crlmm_1.31.2.tar.gz >crlmm.Rcheck\00install.out 2>&1 && cp crlmm.Rcheck\00install.out crlmm-install.out && D:\biocbld\bbs-3.4-bioc\R\bin\R.exe CMD check --library=crlmm.buildbin-libdir --install="check:crlmm-install.out" --force-multiarch --no-vignettes --timings crlmm_1.31.2.tar.gz
StartedAt: 2016-09-20 06:36:43 -0700 (Tue, 20 Sep 2016)
EndedAt: 2016-09-20 06:58:13 -0700 (Tue, 20 Sep 2016)
EllapsedTime: 1290.0 seconds
RetCode: 0
Status:  WARNINGS  
CheckDir: crlmm.Rcheck
Warnings: 1

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   rm -rf crlmm.buildbin-libdir crlmm.Rcheck && mkdir crlmm.buildbin-libdir crlmm.Rcheck && D:\biocbld\bbs-3.4-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=crlmm.buildbin-libdir crlmm_1.31.2.tar.gz >crlmm.Rcheck\00install.out 2>&1 && cp crlmm.Rcheck\00install.out crlmm-install.out  && D:\biocbld\bbs-3.4-bioc\R\bin\R.exe CMD check --library=crlmm.buildbin-libdir --install="check:crlmm-install.out" --force-multiarch --no-vignettes --timings crlmm_1.31.2.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'D:/biocbld/bbs-3.4-bioc/meat/crlmm.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 'crlmm/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'crlmm' version '1.31.2'
* 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 ... OK
* checking for portable file names ... OK
* checking whether package 'crlmm' can be installed ... OK
* checking installed package size ... NOTE
  installed size is  5.0Mb
  sub-directories of 1Mb or more:
    data   2.7Mb
* checking package directory ... OK
* checking 'build' directory ... OK
* checking DESCRIPTION meta-information ... NOTE
Versioned 'LinkingTo' value for 'preprocessCore' is only usable in R >= 3.0.2
* 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
* 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 dependencies in R code ... WARNING
'library' or 'require' call not declared from: 'limma'
'library' or 'require' calls in package code:
  'RUnit' 'limma'
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
Namespaces in Imports field not imported from:
  'SNPchip' 'ff' 'splines'
  All declared Imports should be used.
Unexported object imported by a ':::' call: 'Biobase:::assayDataEnvLock'
  See the note in ?`:::` about the use of this operator.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
.test: no visible global function definition for 'defineTestSuite'
.test: no visible global function definition for 'runTestSuite'
.test: no visible global function definition for 'printTextProtocol'
calculateRBafCNSet : processByChromosome: no visible global function
  definition for 'position'
cnrmaAffy: no visible global function definition for 'celfileName'
computeBR: no visible global function definition for 'genomeBuild'
constructBafLrrSetListFrom: no visible global function definition for
  'genomeBuild'
constructOligoSetListFrom: no visible global function definition for
  'genomeBuild'
genotypeInf: no visible binding for global variable 'anno'
plotSamples: no visible global function definition for 'delete'
quantilenormalization: no visible global function definition for
  'delete'
snprmaAffy: no visible global function definition for 'celfileName'
Undefined global functions or variables:
  anno celfileName defineTestSuite delete genomeBuild position
  printTextProtocol runTestSuite
* 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 line endings in Makefiles ... OK
* checking for GNU extensions in Makefiles ... 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/crlmm.buildbin-libdir/crlmm/libs/i386/crlmm.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
genotype      113.87   2.24  120.93
crlmm         106.79   1.33  113.35
snprma         24.10   0.60   24.71
celfile-utils   3.32   0.25   25.91
** running examples for arch 'x64' ... OK
Examples with CPU or elapsed time > 5s
           user system elapsed
genotype 110.73   2.74  115.56
crlmm    110.02   1.28  111.29
snprma    21.42   0.47   21.91
* checking for unstated dependencies in 'tests' ... OK
* checking tests ...
** running tests for arch 'i386' ...
  Running 'crlmm_unit_tests.R'
  Running 'doRUnit.R'
 OK
** running tests for arch 'x64' ...
  Running 'crlmm_unit_tests.R'
  Running 'doRUnit.R'
 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: 1 WARNING, 4 NOTEs
See
  'D:/biocbld/bbs-3.4-bioc/meat/crlmm.Rcheck/00check.log'
for details.


crlmm.Rcheck/00install.out:


install for i386

* installing *source* package 'crlmm' ...
** libs
C:/Rtools/mingw_32/bin/gcc  -I"D:/biocbld/BBS-3˜1.4-B/R/include" -DNDEBUG    -I"D:/biocbld/bbs-3.4-bioc/R/library/preprocessCore/include" -I"c:/local323/include"     -O3 -Wall  -std=gnu99 -mtune=core2 -c gtypeCaller.c -o gtypeCaller.o
C:/Rtools/mingw_32/bin/gcc  -I"D:/biocbld/BBS-3˜1.4-B/R/include" -DNDEBUG    -I"D:/biocbld/bbs-3.4-bioc/R/library/preprocessCore/include" -I"c:/local323/include"     -O3 -Wall  -std=gnu99 -mtune=core2 -c init.c -o init.o
C:/Rtools/mingw_32/bin/gcc  -I"D:/biocbld/BBS-3˜1.4-B/R/include" -DNDEBUG    -I"D:/biocbld/bbs-3.4-bioc/R/library/preprocessCore/include" -I"c:/local323/include"     -O3 -Wall  -std=gnu99 -mtune=core2 -c trimmed.c -o trimmed.o
C:/Rtools/mingw_32/bin/gcc  -I"D:/biocbld/BBS-3˜1.4-B/R/include" -DNDEBUG    -I"D:/biocbld/bbs-3.4-bioc/R/library/preprocessCore/include" -I"c:/local323/include"     -O3 -Wall  -std=gnu99 -mtune=core2 -c utils.c -o utils.o
C:/Rtools/mingw_32/bin/gcc -shared -s -static-libgcc -o crlmm.dll tmp.def gtypeCaller.o init.o trimmed.o utils.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/crlmm.buildbin-libdir/crlmm/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 'crlmm' ...
** libs
C:/Rtools/mingw_64/bin/gcc  -I"D:/biocbld/BBS-3˜1.4-B/R/include" -DNDEBUG    -I"D:/biocbld/bbs-3.4-bioc/R/library/preprocessCore/include" -I"c:/local323/include"     -O2 -Wall  -std=gnu99 -mtune=core2 -c gtypeCaller.c -o gtypeCaller.o
C:/Rtools/mingw_64/bin/gcc  -I"D:/biocbld/BBS-3˜1.4-B/R/include" -DNDEBUG    -I"D:/biocbld/bbs-3.4-bioc/R/library/preprocessCore/include" -I"c:/local323/include"     -O2 -Wall  -std=gnu99 -mtune=core2 -c init.c -o init.o
C:/Rtools/mingw_64/bin/gcc  -I"D:/biocbld/BBS-3˜1.4-B/R/include" -DNDEBUG    -I"D:/biocbld/bbs-3.4-bioc/R/library/preprocessCore/include" -I"c:/local323/include"     -O2 -Wall  -std=gnu99 -mtune=core2 -c trimmed.c -o trimmed.o
C:/Rtools/mingw_64/bin/gcc  -I"D:/biocbld/BBS-3˜1.4-B/R/include" -DNDEBUG    -I"D:/biocbld/bbs-3.4-bioc/R/library/preprocessCore/include" -I"c:/local323/include"     -O2 -Wall  -std=gnu99 -mtune=core2 -c utils.c -o utils.o
C:/Rtools/mingw_64/bin/gcc -shared -s -static-libgcc -o crlmm.dll tmp.def gtypeCaller.o init.o trimmed.o utils.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/crlmm.buildbin-libdir/crlmm/libs/x64
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'crlmm' as crlmm_1.31.2.zip
* DONE (crlmm)

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

nameusersystemelapsed
ListClassConstructors1.200.021.21
PredictionRegion-class000
batchStatisticAccessors0.340.000.34
calculateRBaf0.910.000.92
celfile-utils 3.32 0.2525.91
cnSetExample0.560.010.58
constructInf000
copynumberAccessors000
crlmm106.79 1.33113.35
genotype.Illumina000
genotype113.87 2.24120.93
genotypeInf000
genotypes000
plotSNPs000
posteriorProbability1.850.111.96
predictionRegion0.440.000.44
preprocessInf000
readGenCallOutput000
readIdatFiles000
snprma24.10 0.6024.71
validCdfNames000
xyplot0.530.010.54

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

nameusersystemelapsed
ListClassConstructors1.510.031.55
PredictionRegion-class000
batchStatisticAccessors0.250.050.29
calculateRBaf1.030.001.03
celfile-utils2.730.182.93
cnSetExample0.490.020.52
constructInf000
copynumberAccessors000
crlmm110.02 1.28111.29
genotype.Illumina000
genotype110.73 2.74115.56
genotypeInf000
genotypes000
plotSNPs000
posteriorProbability1.650.071.71
predictionRegion0.380.000.37
preprocessInf000
readGenCallOutput000
readIdatFiles000
snprma21.42 0.4721.91
validCdfNames000
xyplot0.590.000.59