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BioC 3.0: CHECK report for chimera on moscato1

This page was generated on 2015-04-10 09:48:39 -0700 (Fri, 10 Apr 2015).

Package 145/933HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
chimera 1.8.5
Raffaele A Calogero
Snapshot Date: 2015-04-09 16:20:12 -0700 (Thu, 09 Apr 2015)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_3_0/madman/Rpacks/chimera
Last Changed Rev: 98706 / Revision: 102249
Last Changed Date: 2015-01-26 11:38:47 -0800 (Mon, 26 Jan 2015)
zin1 Linux (Ubuntu 12.04.4 LTS) / x86_64  OK  OK  OK 
moscato1 Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64  OK  OK [ OK ] OK 
perceval Mac OS X Snow Leopard (10.6.8) / x86_64  OK  OK  OK  OK 
oaxaca Mac OS X Mavericks (10.9.5) / x86_64  OK  OK  OK  OK 

Summary

Package: chimera
Version: 1.8.5
Command: rm -rf chimera.buildbin-libdir chimera.Rcheck && mkdir chimera.buildbin-libdir chimera.Rcheck && D:\biocbld\bbs-3.0-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=chimera.buildbin-libdir chimera_1.8.5.tar.gz >chimera.Rcheck\00install.out 2>&1 && cp chimera.Rcheck\00install.out chimera-install.out && D:\biocbld\bbs-3.0-bioc\R\bin\R.exe CMD check --library=chimera.buildbin-libdir --install="check:chimera-install.out" --force-multiarch --no-vignettes --timings chimera_1.8.5.tar.gz
StartedAt: 2015-04-09 23:31:30 -0700 (Thu, 09 Apr 2015)
EndedAt: 2015-04-09 23:49:32 -0700 (Thu, 09 Apr 2015)
EllapsedTime: 1082.1 seconds
RetCode: 0
Status:  OK  
CheckDir: chimera.Rcheck
Warnings: 0

Command output

##############################################################################
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###
### Running command:
###
###   rm -rf chimera.buildbin-libdir chimera.Rcheck && mkdir chimera.buildbin-libdir chimera.Rcheck && D:\biocbld\bbs-3.0-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=chimera.buildbin-libdir chimera_1.8.5.tar.gz >chimera.Rcheck\00install.out 2>&1 && cp chimera.Rcheck\00install.out chimera-install.out  && D:\biocbld\bbs-3.0-bioc\R\bin\R.exe CMD check --library=chimera.buildbin-libdir --install="check:chimera-install.out" --force-multiarch --no-vignettes --timings chimera_1.8.5.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'D:/biocbld/bbs-3.0-bioc/meat/chimera.Rcheck'
* using R version 3.1.3 (2015-03-09)
* using platform: i386-w64-mingw32 (32-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'chimera/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'chimera' version '1.8.5'
* checking package namespace information ... OK
* checking package dependencies ... NOTE
Package which this enhances but not available for checking: 'Rsubread'

Depends: includes the non-default packages:
  'Biobase' 'GenomicRanges' 'Rsamtools' 'GenomicAlignments'
  'AnnotationDbi' 'org.Hs.eg.db' 'BSgenome.Hsapiens.UCSC.hg19'
  'TxDb.Hsapiens.UCSC.hg19.knownGene'
Adding so many packages to the search path is excessive and importing
selectively is preferable.
* 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 'chimera' can be installed ... OK
* checking installed package size ... NOTE
  installed size is  7.5Mb
  sub-directories of 1Mb or more:
    examples   5.7Mb
    libs       1.2Mb
* 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' calls in package code:
  'BSgenome.Mmusculus.UCSC.mm9' 'BiocParallel' 'Rsubread'
  'org.Mm.eg.db'
  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
.buildFusion: no visible global function definition for 'DNAString'
.gfWrap: no visible global function definition for 'writeXStringSet'
.rsImport: no visible global function definition for 'MulticoreParam'
.rsImport: no visible global function definition for 'bplapply'
bam2fastq: no visible global function definition for 'MulticoreParam'
bam2fastq: no visible global function definition for 'bplapply'
chimeraSeqSet: no visible global function definition for
  'MulticoreParam'
chimeraSeqSet: no visible global function definition for 'bplapply'
chimeraSeqSet : <anonymous>: no visible global function definition for
  'DNAStringSet'
chimeraSeqs: no visible global function definition for 'DNAStringSet'
defuseTPTN : .my.newfset: no visible global function definition for
  'DNAStringSet'
filterList: no visible global function definition for 'MulticoreParam'
filterList: no visible global function definition for 'bplapply'
fusionName: no visible global function definition for 'MulticoreParam'
fusionName: no visible global function definition for 'bplapply'
fusionPeptides: no visible global function definition for 'translate'
fusionPeptides: no visible global function definition for 'AAStringSet'
fusionPeptides : <anonymous>: no visible global function definition for
  'pairwiseAlignment'
fusionPeptides: no visible global function definition for 'pattern'
fusionPeptides: no visible global function definition for
  'matchPattern'
gapfillerRun: no visible global function definition for
  'readDNAStringSet'
gapfillerRun: no visible global function definition for
  'pairwiseAlignment'
gapfillerRun: no visible global function definition for 'DNAStringSet'
gapfillerWrap: no visible global function definition for
  'MulticoreParam'
gapfillerWrap: no visible global function definition for 'bplapply'
newfSet: no visible global function definition for 'DNAStringSet'
starReads: no visible global function definition for 'MulticoreParam'
subreadRun: no visible global function definition for 'bowtie_build'
subreadRun: no visible global function definition for 'bowtie'
supportingReads: no visible global function definition for
  'MulticoreParam'
supportingReads: no visible global function definition for 'bplapply'
* 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 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-3.0-bioc/meat/chimera.buildbin-libdir/chimera/libs/i386/chimera.dll':
  Found 'abort', possibly from 'abort' (C), 'runtime' (Fortran)
File 'D:/biocbld/bbs-3.0-bioc/meat/chimera.buildbin-libdir/chimera/libs/x64/chimera.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' ... [379s] OK
Examples with CPU or elapsed time > 5s
                    user system elapsed
plotCoverage       97.75   0.61   98.36
fusionPeptides     83.80   0.99   86.51
chimeraSeqSet      49.81   0.69   52.08
chimeraSeqs        35.71   0.14   35.91
class.fSet         34.34   0.28   34.62
breakpointOverlaps 18.00   0.15   18.26
is.fSet             8.10   0.00    8.09
defuseTPTN          7.97   0.00    7.97
importFusionData    6.24   0.00    6.24
filterList          6.05   0.02    6.07
fusionName          6.04   0.00    6.03
supportingReads     5.65   0.02    5.66
** running examples for arch 'x64' ... [333s] OK
Examples with CPU or elapsed time > 5s
                    user system elapsed
plotCoverage       86.60   0.55   87.14
fusionPeptides     77.54   0.92   78.45
chimeraSeqSet      39.43   0.36   39.78
class.fSet         26.16   0.03   26.20
chimeraSeqs        25.28   0.22   25.50
breakpointOverlaps 16.11   0.17   16.29
filterList          8.33   0.00    8.33
defuseTPTN          8.21   0.00    8.22
importFusionData    7.43   0.00    7.42
supportingReads     7.38   0.00    7.38
fusionName          7.22   0.01    7.24
is.fSet             6.77   0.00    6.77
* checking for unstated dependencies in vignettes ... NOTE
'library' or 'require' call not declared from: 'xtable'
* 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

NOTE: There were 6 notes.
See
  'D:/biocbld/bbs-3.0-bioc/meat/chimera.Rcheck/00check.log'
for details.

chimera.Rcheck/00install.out:


install for i386

* installing *source* package 'chimera' ...
** libs
g++ -m32 -I"D:/biocbld/BBS-3˜1.0-B/R/include" -DNDEBUG     -I"d:/RCompile/CRANpkg/extralibs64/local/include"     -O2 -Wall  -mtune=core2 -c StarParser.cpp -o StarParser.o
g++ -m32 -shared -s -static-libgcc -o chimera.dll tmp.def StarParser.o -Ld:/RCompile/CRANpkg/extralibs64/local/lib/i386 -Ld:/RCompile/CRANpkg/extralibs64/local/lib -LD:/biocbld/BBS-3˜1.0-B/R/bin/i386 -lR
installing to D:/biocbld/bbs-3.0-bioc/meat/chimera.buildbin-libdir/chimera/libs/i386
** R
** 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 'chimera' ...
** libs
g++ -m64 -I"D:/biocbld/BBS-3˜1.0-B/R/include" -DNDEBUG     -I"d:/RCompile/CRANpkg/extralibs64/local/include"     -O2 -Wall  -mtune=core2 -c StarParser.cpp -o StarParser.o
g++ -m64 -shared -s -static-libgcc -o chimera.dll tmp.def StarParser.o -Ld:/RCompile/CRANpkg/extralibs64/local/lib/x64 -Ld:/RCompile/CRANpkg/extralibs64/local/lib -LD:/biocbld/BBS-3˜1.0-B/R/bin/x64 -lR
installing to D:/biocbld/bbs-3.0-bioc/meat/chimera.buildbin-libdir/chimera/libs/x64
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'chimera' as chimera_1.8.5.zip
* DONE (chimera)

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

nameusersystemelapsed
MHmakeRandomString000
bam2fastq000
breakpointOverlaps18.00 0.1518.26
chimeraSeqSet49.81 0.6952.08
chimeraSeqs35.71 0.1435.91
class.fSet34.34 0.2834.62
defuseTPTN7.970.007.97
filterList6.050.026.07
filterSamReads000
fusionName6.040.006.03
fusionPeptides83.80 0.9986.51
gapfillerInstallation000
gapfillerRun000
gapfillerWrap000
importFusionData6.240.006.24
is.fSet8.100.008.09
newfSet0.050.000.05
oncofuseInstallation0.010.000.01
oncofuseRun000
picardInstallation000
plotCoverage97.75 0.6198.36
prettyPrint000
removingErrorLine000
starInstallation000
starReads000
starRun000
subreadRun0.020.000.02
supportingReads5.650.025.66
tophatInstallation000
tophatRun0.020.000.01
validateSamFile000

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

nameusersystemelapsed
MHmakeRandomString000
bam2fastq000
breakpointOverlaps16.11 0.1716.29
chimeraSeqSet39.43 0.3639.78
chimeraSeqs25.28 0.2225.50
class.fSet26.16 0.0326.20
defuseTPTN8.210.008.22
filterList8.330.008.33
filterSamReads000
fusionName7.220.017.24
fusionPeptides77.54 0.9278.45
gapfillerInstallation000
gapfillerRun000
gapfillerWrap000
importFusionData7.430.007.42
is.fSet6.770.006.77
newfSet0.070.000.06
oncofuseInstallation000
oncofuseRun000
picardInstallation000
plotCoverage86.60 0.5587.14
prettyPrint000
removingErrorLine000
starInstallation000
starReads000
starRun000
subreadRun000
supportingReads7.380.007.38
tophatInstallation000
tophatRun000
validateSamFile000