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BioC 3.0: CHECK report for h5vc on moscato1

This page was generated on 2015-04-10 09:49:49 -0700 (Fri, 10 Apr 2015).

Package 416/933HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
h5vc 2.0.6
Paul Theodor Pyl
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/h5vc
Last Changed Rev: 98471 / Revision: 102249
Last Changed Date: 2015-01-19 10:34:46 -0800 (Mon, 19 Jan 2015)
zin1 Linux (Ubuntu 12.04.4 LTS) / x86_64  NotNeeded  OK  WARNINGS 
moscato1 Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64  NotNeeded  OK [ WARNINGS ] OK 
perceval Mac OS X Snow Leopard (10.6.8) / x86_64  NotNeeded  OK  WARNINGS  OK 
oaxaca Mac OS X Mavericks (10.9.5) / x86_64  NotNeeded  OK  WARNINGS  OK 

Summary

Package: h5vc
Version: 2.0.6
Command: rm -rf h5vc.buildbin-libdir h5vc.Rcheck && mkdir h5vc.buildbin-libdir h5vc.Rcheck && D:\biocbld\bbs-3.0-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=h5vc.buildbin-libdir h5vc_2.0.6.tar.gz >h5vc.Rcheck\00install.out 2>&1 && cp h5vc.Rcheck\00install.out h5vc-install.out && D:\biocbld\bbs-3.0-bioc\R\bin\R.exe CMD check --library=h5vc.buildbin-libdir --install="check:h5vc-install.out" --force-multiarch --no-vignettes --timings h5vc_2.0.6.tar.gz
StartedAt: 2015-04-10 02:05:57 -0700 (Fri, 10 Apr 2015)
EndedAt: 2015-04-10 02:14:27 -0700 (Fri, 10 Apr 2015)
EllapsedTime: 510.6 seconds
RetCode: 0
Status:  WARNINGS  
CheckDir: h5vc.Rcheck
Warnings: 1

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   rm -rf h5vc.buildbin-libdir h5vc.Rcheck && mkdir h5vc.buildbin-libdir h5vc.Rcheck && D:\biocbld\bbs-3.0-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=h5vc.buildbin-libdir h5vc_2.0.6.tar.gz >h5vc.Rcheck\00install.out 2>&1 && cp h5vc.Rcheck\00install.out h5vc-install.out  && D:\biocbld\bbs-3.0-bioc\R\bin\R.exe CMD check --library=h5vc.buildbin-libdir --install="check:h5vc-install.out" --force-multiarch --no-vignettes --timings h5vc_2.0.6.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'D:/biocbld/bbs-3.0-bioc/meat/h5vc.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 'h5vc/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'h5vc' version '2.0.6'
* 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 'h5vc' 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 ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
.h5dapplyIRanges: no visible binding for global variable 'Sample'
callVariantsPairedFisher : <anonymous> : <anonymous>: no visible
  binding for global variable 'pValue'
callVariantsPairedFisher : <anonymous> : <anonymous>: no visible
  binding for global variable 'BlockID'
callVariantsSingle : <anonymous> : <anonymous>: no visible binding for
  global variable 'Support'
callVariantsSingle : <anonymous> : <anonymous>: no visible binding for
  global variable 'AF'
callVariantsSingle : <anonymous> : <anonymous>: no visible binding for
  global variable 'SupFwd'
callVariantsSingle : <anonymous> : <anonymous>: no visible binding for
  global variable 'SupRev'
callVariantsSingle : <anonymous> : <anonymous>: no visible binding for
  global variable 'BlockID'
h5readBlock: no visible binding for global variable 'Sample'
mergeTallyFiles : <anonymous>: no visible binding for global variable
  'group'
mergeTallyFiles: no visible binding for global variable 'SourceFile'
plotMutationSpectrum: no visible binding for global variable
  'altAllele'
plotMutationSpectrum: no visible binding for global variable 'tmp'
rerunBatchTallies: no visible binding for global variable 'regID'
resizeCohort: no visible binding for global variable 'newSamples'
tallyRangesBatch : <anonymous>: no visible binding for global variable
  'bamFiles'
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... WARNING
Codoc mismatches from documentation object 'callVariants':
vcConfParams
  Code: function(minStrandCov = 5, maxStrandCov = 200,
                 minStrandAltSupport = 2, maxStrandAltSupportControl =
                 0, minStrandDelSupport = minStrandAltSupport,
                 maxStrandDelSupportControl =
                 maxStrandAltSupportControl, minStrandInsSupport =
                 minStrandAltSupport, maxStrandInsSupportControl =
                 maxStrandAltSupportControl, minStrandCovControl = 5,
                 maxStrandCovControl = 200, bases = 5:8,
                 returnDataPoints = TRUE, annotateWithBackground =
                 TRUE, mergeCalls = TRUE, mergeAggregator = mean,
                 pValueAggregator = max)
  Docs: function(minStrandCov = 5, maxStrandCov = 200,
                 minStrandAltSupport = 2, maxStrandAltSupportControl =
                 0, minStrandDelSupport = minStrandAltSupport,
                 maxStrandDelSupportControl =
                 maxStrandAltSupportControl, minStrandCovControl = 5,
                 maxStrandCovControl = 200, bases = 5:8,
                 returnDataPoints = TRUE, annotateWithBackground =
                 TRUE, mergeCalls = TRUE, mergeAggregator = mean,
                 pValueAggregator = max)
  Argument names in code not in docs:
    minStrandInsSupport maxStrandInsSupportControl
  Mismatches in argument names (first 3):
    Position: 7 Code: minStrandInsSupport Docs: minStrandCovControl
    Position: 8 Code: maxStrandInsSupportControl Docs: maxStrandCovControl
    Position: 9 Code: minStrandCovControl Docs: bases

* 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 compilation flags in Makevars ... OK
* checking for GNU extensions in Makefiles ... OK
* checking for portable use of $(BLAS_LIBS) and $(LAPACK_LIBS) ... 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/h5vc.buildbin-libdir/h5vc/libs/i386/h5vc.dll':
  Found 'abort', possibly from 'abort' (C), 'runtime' (Fortran)
  Found 'puts', possibly from 'printf' (C), 'puts' (C)
  Found 'rand', possibly from 'rand' (C)
File 'D:/biocbld/bbs-3.0-bioc/meat/h5vc.buildbin-libdir/h5vc/libs/x64/h5vc.dll':
  Found 'abort', possibly from 'abort' (C), 'runtime' (Fortran)
  Found 'puts', possibly from 'printf' (C), 'puts' (C)
  Found 'rand', possibly from 'rand' (C)

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' ... [118s] OK
Examples with CPU or elapsed time > 5s
                    user system elapsed
callVariantsFisher 18.46   0.05   18.50
applyTallies       13.31   0.63   14.25
mergeTallies       10.42   0.52   10.94
prepareForHDF5     10.00   0.69   10.70
writeToTallyFile    8.42   0.33    8.75
mismatchPlot        6.55   0.10    6.66
tallyRanges         5.40   0.23   14.98
binnedAFs           4.09   0.06    6.29
** running examples for arch 'x64' ... [120s] OK
Examples with CPU or elapsed time > 5s
                    user system elapsed
callVariantsFisher 24.66   0.03   24.70
applyTallies       16.10   0.98   17.09
mergeTallies       11.52   0.88   12.40
prepareForHDF5     10.77   0.94   11.70
mismatchPlot        8.95   0.06    9.27
writeToTallyFile    7.60   0.40    8.01
binnedAFs           5.18   0.12    5.47
* 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

WARNING: There was 1 warning.
NOTE: There were 2 notes.
See
  'D:/biocbld/bbs-3.0-bioc/meat/h5vc.Rcheck/00check.log'
for details.

h5vc.Rcheck/00install.out:


install for i386

* installing *source* package 'h5vc' ...
** libs
g++ -m32 -I"D:/biocbld/bbs-3.0-bioc/R/library/zlibbioc/include" -I"D:/biocbld/BBS-3˜1.0-B/R/include" -DNDEBUG -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -ID:/biocbld/bbs-3.0-bioc/R/library/Rsamtools/include -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE    -I"d:/RCompile/CRANpkg/extralibs64/local/include"     -O2 -Wall  -mtune=core2 -c tallyBAM.cpp -o tallyBAM.o
tallyBAM.cpp: In function 'int pileup_func_old(uint32_t, uint32_t, int, const bam_pileup1_t*, void*)':
tallyBAM.cpp:47:7: warning: unused variable 'len' [-Wunused-variable]
tallyBAM.cpp: In function 'int pileup_func(uint32_t, uint32_t, int, const bam_pileup1_t*, void*)':
tallyBAM.cpp:96:7: warning: unused variable 'len' [-Wunused-variable]
tallyBAM.cpp: In function 'int _tallyBAM(char**, char**, int*, int*, int*, int*, int*, int*, int*, int*)':
tallyBAM.cpp:141:6: warning: unused variable 'c' [-Wunused-variable]
tallyBAM.cpp: At global scope:
tallyBAM.cpp:43:12: warning: 'int pileup_func_old(uint32_t, uint32_t, int, const bam_pileup1_t*, void*)' defined but not used [-Wunused-function]
g++ -m32 -shared -s -static-libgcc -o h5vc.dll tmp.def tallyBAM.o D:/biocbld/bbs-3.0-bioc/R/library/Rsamtools/usrlib/i386/libbam.a D:/biocbld/bbs-3.0-bioc/R/library/Rsamtools/usrlib/i386/libbam.a D:/biocbld/bbs-3.0-bioc/R/library/Rsamtools/usrlib/i386/libbcf.a D:/biocbld/bbs-3.0-bioc/R/library/Rsamtools/usrlib/i386/libtabix.a -lws2_32 -pthread -LD:/biocbld/bbs-3.0-bioc/R/library/zlibbioc/libs/i386 -lzlib1bioc -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/h5vc.buildbin-libdir/h5vc/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 'h5vc' ...
** libs
g++ -m64 -I"D:/biocbld/bbs-3.0-bioc/R/library/zlibbioc/include" -I"D:/biocbld/BBS-3˜1.0-B/R/include" -DNDEBUG -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -ID:/biocbld/bbs-3.0-bioc/R/library/Rsamtools/include -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE    -I"d:/RCompile/CRANpkg/extralibs64/local/include"     -O2 -Wall  -mtune=core2 -c tallyBAM.cpp -o tallyBAM.o
tallyBAM.cpp: In function 'int pileup_func_old(uint32_t, uint32_t, int, const bam_pileup1_t*, void*)':
tallyBAM.cpp:47:7: warning: unused variable 'len' [-Wunused-variable]
tallyBAM.cpp: In function 'int pileup_func(uint32_t, uint32_t, int, const bam_pileup1_t*, void*)':
tallyBAM.cpp:96:7: warning: unused variable 'len' [-Wunused-variable]
tallyBAM.cpp: In function 'int _tallyBAM(char**, char**, int*, int*, int*, int*, int*, int*, int*, int*)':
tallyBAM.cpp:141:6: warning: unused variable 'c' [-Wunused-variable]
tallyBAM.cpp: At global scope:
tallyBAM.cpp:43:12: warning: 'int pileup_func_old(uint32_t, uint32_t, int, const bam_pileup1_t*, void*)' defined but not used [-Wunused-function]
g++ -m64 -shared -s -static-libgcc -o h5vc.dll tmp.def tallyBAM.o D:/biocbld/bbs-3.0-bioc/R/library/Rsamtools/usrlib/x64/libbam.a D:/biocbld/bbs-3.0-bioc/R/library/Rsamtools/usrlib/x64/libbam.a D:/biocbld/bbs-3.0-bioc/R/library/Rsamtools/usrlib/x64/libbcf.a D:/biocbld/bbs-3.0-bioc/R/library/Rsamtools/usrlib/x64/libtabix.a -lws2_32 -pthread -LD:/biocbld/bbs-3.0-bioc/R/library/zlibbioc/libs/x64 -lzlib1bioc -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/h5vc.buildbin-libdir/h5vc/libs/x64
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'h5vc' as h5vc_2.0.6.zip
* DONE (h5vc)

h5vc.Rcheck/examples_i386/h5vc-Ex.timings:

nameusersystemelapsed
applyTallies13.31 0.6314.25
batchTallies000
binGenome0.430.070.66
binnedAFs4.090.066.29
callVariants0.980.052.65
callVariantsFisher18.46 0.0518.50
callVariantsSingle1.480.071.56
coverage3.650.104.10
geom_h5vc1.020.041.07
getSampleData0.120.000.12
h5dapply1.110.021.12
h5readBlock0.280.001.39
helpers0.190.030.22
mergeTallies10.42 0.5210.94
mergeTallyFiles000
mismatchPlot6.550.106.66
mutationSpectrum1.460.042.08
plotMutationSpectrum3.070.213.29
prepareForHDF510.00 0.6910.70
prepareTallyFile0.070.000.06
tallyBAM0.170.000.17
tallyRanges 5.40 0.2314.98
writeReference0.300.020.35
writeToTallyFile8.420.338.75

h5vc.Rcheck/examples_x64/h5vc-Ex.timings:

nameusersystemelapsed
applyTallies16.10 0.9817.09
batchTallies000
binGenome0.510.050.56
binnedAFs5.180.125.47
callVariants1.000.011.01
callVariantsFisher24.66 0.0324.70
callVariantsSingle1.940.001.93
coverage3.640.103.73
geom_h5vc0.900.000.92
getSampleData0.120.000.13
h5dapply1.470.011.50
h5readBlock0.250.000.25
helpers0.190.030.22
mergeTallies11.52 0.8812.40
mergeTallyFiles000
mismatchPlot8.950.069.27
mutationSpectrum0.920.060.99
plotMutationSpectrum2.510.112.62
prepareForHDF510.77 0.9411.70
prepareTallyFile0.070.000.22
tallyBAM0.190.000.18
tallyRanges4.620.224.84
writeReference0.630.110.74
writeToTallyFile7.600.408.01