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BioC 3.2: CHECK report for cn.mops on moscato1

This page was generated on 2015-08-20 13:20:35 -0700 (Thu, 20 Aug 2015).

Package 189/1069HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
cn.mops 1.15.3
Guenter Klambauer
Snapshot Date: 2015-08-19 16:24:33 -0700 (Wed, 19 Aug 2015)
URL: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/cn.mops
Last Changed Rev: 106321 / Revision: 107602
Last Changed Date: 2015-07-14 00:47:30 -0700 (Tue, 14 Jul 2015)
zin1 Linux (Ubuntu 14.04.2 LTS) / x86_64  OK  OK  OK UNNEEDED, same version exists in internal repository
moscato1 Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64  OK  OK [ OK ] OK UNNEEDED, same version exists in internal repository
perceval Mac OS X Snow Leopard (10.6.8) / x86_64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository
oaxaca Mac OS X Mavericks (10.9.5) / x86_64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: cn.mops
Version: 1.15.3
Command: rm -rf cn.mops.buildbin-libdir cn.mops.Rcheck && mkdir cn.mops.buildbin-libdir cn.mops.Rcheck && D:\biocbld\bbs-3.2-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=cn.mops.buildbin-libdir cn.mops_1.15.3.tar.gz >cn.mops.Rcheck\00install.out 2>&1 && cp cn.mops.Rcheck\00install.out cn.mops-install.out && D:\biocbld\bbs-3.2-bioc\R\bin\R.exe CMD check --library=cn.mops.buildbin-libdir --install="check:cn.mops-install.out" --force-multiarch --no-vignettes --timings cn.mops_1.15.3.tar.gz
StartedAt: 2015-08-20 02:50:53 -0700 (Thu, 20 Aug 2015)
EndedAt: 2015-08-20 03:00:17 -0700 (Thu, 20 Aug 2015)
EllapsedTime: 564.1 seconds
RetCode: 0
Status:  OK  
CheckDir: cn.mops.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   rm -rf cn.mops.buildbin-libdir cn.mops.Rcheck && mkdir cn.mops.buildbin-libdir cn.mops.Rcheck && D:\biocbld\bbs-3.2-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=cn.mops.buildbin-libdir cn.mops_1.15.3.tar.gz >cn.mops.Rcheck\00install.out 2>&1 && cp cn.mops.Rcheck\00install.out cn.mops-install.out  && D:\biocbld\bbs-3.2-bioc\R\bin\R.exe CMD check --library=cn.mops.buildbin-libdir --install="check:cn.mops-install.out" --force-multiarch --no-vignettes --timings cn.mops_1.15.3.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'D:/biocbld/bbs-3.2-bioc/meat/cn.mops.Rcheck'
* using R version 3.2.2 (2015-08-14)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'cn.mops/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'cn.mops' version '1.15.3'
* 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 'cn.mops' can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking 'build' directory ... OK
* checking DESCRIPTION meta-information ... OK
* 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 ... NOTE
'library' or 'require' call to 'DNAcopy' in package code.
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
Package in Depends field not imported from: 'BiocGenerics'
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
.convertToFastSegRes: no visible global function definition for
  'subjectHits'
.convertToFastSegRes: no visible global function definition for
  'values<-'
.makeLogRatios: no visible global function definition for 'rowMedians'
.makeLogRatios: no visible global function definition for 'values<-'
.replaceNames: no visible global function definition for 'values<-'
.segPlot: no visible global function definition for 'seqnames'
.segPlot: no visible global function definition for 'ranges'
cn.mops: no visible global function definition for 'strand'
cn.mops: no visible global function definition for 'seqnames'
cn.mops: no visible global function definition for 'GRanges'
cn.mops: no visible global function definition for 'seqinfo'
cn.mops: no visible global function definition for 'sortSeqlevels'
cn.mops: no visible global function definition for 'reduce'
cn.mops: no visible global function definition for 'values<-'
getReadCountsFromBAM: no visible global function definition for
  'sortSeqlevels'
getReadCountsFromBAM: no visible global function definition for
  'seqlengths<-'
getReadCountsFromBAM: no visible global function definition for
  'seqlevels'
haplocn.mops: no visible global function definition for 'strand'
haplocn.mops: no visible global function definition for 'seqnames'
haplocn.mops: no visible global function definition for 'GRanges'
haplocn.mops: no visible global function definition for 'seqinfo'
haplocn.mops: no visible global function definition for 'sortSeqlevels'
haplocn.mops: no visible global function definition for 'reduce'
normalizeChromosomes: no visible global function definition for
  'seqnames'
normalizeChromosomes: no visible global function definition for
  'values<-'
normalizeGenome: no visible global function definition for 'values<-'
referencecn.mops: no visible global function definition for 'strand'
referencecn.mops: no visible global function definition for 'seqnames'
referencecn.mops: no visible global function definition for 'GRanges'
referencecn.mops: no visible global function definition for 'seqinfo'
referencecn.mops: no visible global function definition for
  'sortSeqlevels'
referencecn.mops: no visible global function definition for 'reduce'
referencecn.mops: no visible global function definition for 'values<-'
singlecn.mops: no visible global function definition for 'GRanges'
singlecn.mops: no visible global function definition for 'strand'
singlecn.mops: no visible global function definition for 'seqnames'
singlecn.mops: no visible global function definition for 'seqinfo'
singlecn.mops: no visible global function definition for
  'sortSeqlevels'
calcIntegerCopyNumbers,CNVDetectionResult: no visible global function
  definition for 'values<-'
individualCall,CNVDetectionResult: no visible global function
  definition for 'values<-'
iniCall,CNVDetectionResult: no visible global function definition for
  'values<-'
integerCopyNumber,CNVDetectionResult: no visible global function
  definition for 'values<-'
localAssessments,CNVDetectionResult: no visible global function
  definition for 'values<-'
makeRobustCNVR,CNVDetectionResult: no visible global function
  definition for 'seqnames'
makeRobustCNVR,CNVDetectionResult: no visible global function
  definition for 'GRanges'
makeRobustCNVR,CNVDetectionResult: no visible global function
  definition for 'values<-'
makeRobustCNVR,CNVDetectionResult: no visible global function
  definition for 'reduce'
normalizedData,CNVDetectionResult: no visible global function
  definition for 'values<-'
plot,CNVDetectionResult-missing : .local: no visible global function
  definition for 'GRanges'
plot,CNVDetectionResult-missing : .local: no visible global function
  definition for 'seqnames'
plot,CNVDetectionResult-missing : .local: no visible global function
  definition for 'rowMedians'
segplot,CNVDetectionResult: no visible global function definition for
  'sampleNames'
* 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-3.2-bioc/meat/cn.mops.buildbin-libdir/cn.mops/libs/i386/cn.mops.dll':
  Found 'abort', possibly from 'abort' (C), 'runtime' (Fortran)
File 'D:/biocbld/bbs-3.2-bioc/meat/cn.mops.buildbin-libdir/cn.mops/libs/x64/cn.mops.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' ... [184s] OK
Examples with CPU or elapsed time > 5s
                                                     user system elapsed
referencecn.mops                                    34.74   0.00   54.32
calcFractionalCopyNumbers-CNVDetectionResult-method 21.50   0.00   21.49
calcFractionalCopyNumbers                           21.11   0.02   21.13
cn.mops                                             14.91   0.19   31.59
exomecn.mops                                         5.92   0.00    5.91
haplocn.mops                                         1.86   0.03   14.70
getReadCountsFromBAM                                 0.18   0.00    6.05
** running examples for arch 'x64' ... [182s] OK
Examples with CPU or elapsed time > 5s
                                                     user system elapsed
referencecn.mops                                    26.44   0.00   50.84
cn.mops                                             17.15   0.28   35.47
calcFractionalCopyNumbers                           17.00   0.02   17.01
calcFractionalCopyNumbers-CNVDetectionResult-method 16.49   0.01   16.51
exomecn.mops                                         6.52   0.00    6.54
haplocn.mops                                         2.39   0.02   15.59
getReadCountsFromBAM                                 0.16   0.01    6.10
getSegmentReadCountsFromBAM                          0.11   0.00    6.04
* 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: 3 NOTEs
See
  'D:/biocbld/bbs-3.2-bioc/meat/cn.mops.Rcheck/00check.log'
for details.


cn.mops.Rcheck/00install.out:


install for i386

* installing *source* package 'cn.mops' ...
** libs
gcc -m32 -I"D:/biocbld/BBS-3˜1.2-B/R/include" -DNDEBUG     -I"d:/RCompile/r-compiling/local/local320/include"     -O3 -Wall  -std=gnu99 -mtune=core2 -c R_init_cnmops.c -o R_init_cnmops.o
g++ -m32 -I"D:/biocbld/BBS-3˜1.2-B/R/include" -DNDEBUG     -I"d:/RCompile/r-compiling/local/local320/include"     -O2 -Wall  -mtune=core2 -c cnmops.cpp -o cnmops.o
g++ -m32 -I"D:/biocbld/BBS-3˜1.2-B/R/include" -DNDEBUG     -I"d:/RCompile/r-compiling/local/local320/include"     -O2 -Wall  -mtune=core2 -c segment.cpp -o segment.o
segment.cpp: In function 'SEXPREC* segment(SEXP, SEXP, SEXP, SEXP, SEXP, SEXP)':
segment.cpp:59:20: warning: variable 'globalSd' set but not used [-Wunused-but-set-variable]
segment.cpp:60:9: warning: variable 'oldStatistic' set but not used [-Wunused-but-set-variable]
segment.cpp:61:31: warning: variable 'maxStatistic' set but not used [-Wunused-but-set-variable]
segment.cpp:62:40: warning: variable 'maxIdx' set but not used [-Wunused-but-set-variable]
segment.cpp:64:9: warning: unused variable 'Rf_beta' [-Wunused-variable]
g++ -m32 -shared -s -static-libgcc -o cn.mops.dll tmp.def R_init_cnmops.o cnmops.o segment.o -Ld:/RCompile/r-compiling/local/local320/lib/i386 -Ld:/RCompile/r-compiling/local/local320/lib -LD:/biocbld/BBS-3˜1.2-B/R/bin/i386 -lR
installing to D:/biocbld/bbs-3.2-bioc/meat/cn.mops.buildbin-libdir/cn.mops/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 'cn.mops' ...
** libs
gcc -m64 -I"D:/biocbld/BBS-3˜1.2-B/R/include" -DNDEBUG     -I"d:/RCompile/r-compiling/local/local320/include"     -O2 -Wall  -std=gnu99 -mtune=core2 -c R_init_cnmops.c -o R_init_cnmops.o
g++ -m64 -I"D:/biocbld/BBS-3˜1.2-B/R/include" -DNDEBUG     -I"d:/RCompile/r-compiling/local/local320/include"     -O2 -Wall  -mtune=core2 -c cnmops.cpp -o cnmops.o
g++ -m64 -I"D:/biocbld/BBS-3˜1.2-B/R/include" -DNDEBUG     -I"d:/RCompile/r-compiling/local/local320/include"     -O2 -Wall  -mtune=core2 -c segment.cpp -o segment.o
segment.cpp: In function 'SEXPREC* segment(SEXP, SEXP, SEXP, SEXP, SEXP, SEXP)':
segment.cpp:59:20: warning: variable 'globalSd' set but not used [-Wunused-but-set-variable]
segment.cpp:60:9: warning: variable 'oldStatistic' set but not used [-Wunused-but-set-variable]
segment.cpp:61:31: warning: variable 'maxStatistic' set but not used [-Wunused-but-set-variable]
segment.cpp:62:40: warning: variable 'maxIdx' set but not used [-Wunused-but-set-variable]
segment.cpp:64:9: warning: unused variable 'Rf_beta' [-Wunused-variable]
g++ -m64 -shared -s -static-libgcc -o cn.mops.dll tmp.def R_init_cnmops.o cnmops.o segment.o -Ld:/RCompile/r-compiling/local/local320/lib/x64 -Ld:/RCompile/r-compiling/local/local320/lib -LD:/biocbld/BBS-3˜1.2-B/R/bin/x64 -lR
installing to D:/biocbld/bbs-3.2-bioc/meat/cn.mops.buildbin-libdir/cn.mops/libs/x64
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'cn.mops' as cn.mops_1.15.3.zip
* DONE (cn.mops)

cn.mops.Rcheck/examples_i386/cn.mops-Ex.timings:

nameusersystemelapsed
CNVDetectionResult000
calcFractionalCopyNumbers-CNVDetectionResult-method21.50 0.0021.49
calcFractionalCopyNumbers21.11 0.0221.13
calcIntegerCopyNumbers-CNVDetectionResult-method0.510.000.51
calcIntegerCopyNumbers0.520.000.52
cn.mops14.91 0.1931.59
cnvr-CNVDetectionResult-method0.420.000.42
cnvr0.490.000.48
cnvs-CNVDetectionResult-method0.370.000.38
cnvs0.340.000.34
exomecn.mops5.920.005.91
getReadCountsFromBAM0.180.006.05
getSegmentReadCountsFromBAM0.080.004.79
gr-CNVDetectionResult-method0.350.000.35
gr0.540.000.54
haplocn.mops 1.86 0.0314.70
individualCall-CNVDetectionResult-method0.560.000.56
individualCall0.420.000.42
iniCall-CNVDetectionResult-method0.420.000.42
iniCall0.420.000.42
integerCopyNumber-CNVDetectionResult-method0.440.000.44
integerCopyNumber0.480.000.48
localAssessments-CNVDetectionResult-method0.380.000.38
localAssessments0.390.000.39
makeRobustCNVR0.570.000.58
normalizeChromosomes0.480.000.48
normalizeGenome0.690.010.71
normalizedData-CNVDetectionResult-method0.390.020.40
normalizedData0.410.000.41
params-CNVDetectionResult-method0.350.000.36
params0.530.000.53
posteriorProbs-CNVDetectionResult-method0.280.000.28
posteriorProbs0.440.020.46
referencecn.mops34.74 0.0054.32
sampleNames-CNVDetectionResult-method0.410.010.42
sampleNames0.350.000.36
segment0.040.000.03
segmentation-CNVDetectionResult-method0.390.000.39
segmentation0.320.030.36
segplot-CNVDetectionResult-method1.950.001.95
segplot1.480.021.49
singlecn.mops1.330.001.33

cn.mops.Rcheck/examples_x64/cn.mops-Ex.timings:

nameusersystemelapsed
CNVDetectionResult000
calcFractionalCopyNumbers-CNVDetectionResult-method16.49 0.0116.51
calcFractionalCopyNumbers17.00 0.0217.01
calcIntegerCopyNumbers-CNVDetectionResult-method0.660.000.66
calcIntegerCopyNumbers0.820.000.83
cn.mops17.15 0.2835.47
cnvr-CNVDetectionResult-method0.580.000.57
cnvr0.530.000.53
cnvs-CNVDetectionResult-method0.470.000.47
cnvs0.50.00.5
exomecn.mops6.520.006.54
getReadCountsFromBAM0.160.016.10
getSegmentReadCountsFromBAM0.110.006.04
gr-CNVDetectionResult-method0.560.020.57
gr0.590.000.61
haplocn.mops 2.39 0.0215.59
individualCall-CNVDetectionResult-method0.450.000.45
individualCall0.380.000.38
iniCall-CNVDetectionResult-method0.470.000.47
iniCall0.530.010.54
integerCopyNumber-CNVDetectionResult-method0.70.00.7
integerCopyNumber0.590.020.61
localAssessments-CNVDetectionResult-method0.420.010.44
localAssessments0.420.020.44
makeRobustCNVR0.550.000.54
normalizeChromosomes0.480.000.49
normalizeGenome0.430.010.43
normalizedData-CNVDetectionResult-method0.420.020.44
normalizedData0.430.000.44
params-CNVDetectionResult-method0.470.000.46
params0.420.000.43
posteriorProbs-CNVDetectionResult-method0.380.000.37
posteriorProbs0.390.000.39
referencecn.mops26.44 0.0050.84
sampleNames-CNVDetectionResult-method0.760.000.76
sampleNames0.50.00.5
segment0.040.000.05
segmentation-CNVDetectionResult-method0.520.010.53
segmentation0.470.000.46
segplot-CNVDetectionResult-method2.010.002.02
segplot2.260.002.26
singlecn.mops1.470.021.48