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BioC 3.6: CHECK report for biovizBase on tokay1

This page was generated on 2017-08-16 13:29:58 -0400 (Wed, 16 Aug 2017).

Package 139/1410HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
biovizBase 1.25.1
Michael Lawrence
Snapshot Date: 2017-08-15 17:18:21 -0400 (Tue, 15 Aug 2017)
URL: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/biovizBase
Last Changed Rev: 129281 / Revision: 131943
Last Changed Date: 2017-04-29 16:26:34 -0400 (Sat, 29 Apr 2017)
malbec1 Linux (Ubuntu 16.04.1 LTS) / x86_64  OK  OK  OK UNNEEDED, same version exists in internal repository
tokay1 Windows Server 2012 R2 Standard / x64  OK  OK [ OK ] OK UNNEEDED, same version exists in internal repository
veracruz1 OS X 10.11.6 El Capitan / x86_64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: biovizBase
Version: 1.25.1
Command: rm -rf biovizBase.buildbin-libdir biovizBase.Rcheck && mkdir biovizBase.buildbin-libdir biovizBase.Rcheck && C:\Users\biocbuild\bbs-3.6-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=biovizBase.buildbin-libdir biovizBase_1.25.1.tar.gz >biovizBase.Rcheck\00install.out 2>&1 && cp biovizBase.Rcheck\00install.out biovizBase-install.out && C:\Users\biocbuild\bbs-3.6-bioc\R\bin\R.exe CMD check --library=biovizBase.buildbin-libdir --install="check:biovizBase-install.out" --force-multiarch --no-vignettes --timings biovizBase_1.25.1.tar.gz
StartedAt: 2017-08-15 22:03:50 -0400 (Tue, 15 Aug 2017)
EndedAt: 2017-08-15 22:11:15 -0400 (Tue, 15 Aug 2017)
EllapsedTime: 444.5 seconds
RetCode: 0
Status:  OK  
CheckDir: biovizBase.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   rm -rf biovizBase.buildbin-libdir biovizBase.Rcheck && mkdir biovizBase.buildbin-libdir biovizBase.Rcheck && C:\Users\biocbuild\bbs-3.6-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=biovizBase.buildbin-libdir biovizBase_1.25.1.tar.gz >biovizBase.Rcheck\00install.out 2>&1 && cp biovizBase.Rcheck\00install.out biovizBase-install.out  &&  C:\Users\biocbuild\bbs-3.6-bioc\R\bin\R.exe CMD check --library=biovizBase.buildbin-libdir --install="check:biovizBase-install.out" --force-multiarch --no-vignettes --timings biovizBase_1.25.1.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'C:/Users/biocbuild/bbs-3.6-bioc/meat/biovizBase.Rcheck'
* using R version 3.4.1 (2017-06-30)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'biovizBase/DESCRIPTION' ... OK
* this is package 'biovizBase' version '1.25.1'
* 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 'biovizBase' can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking 'build' directory ... OK
* checking DESCRIPTION meta-information ... NOTE
Malformed Title field: should not end in a period.
* 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' 'rtracklayer'
  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
genSymbols: no visible binding for global variable 'start_location'
genSymbols: no visible binding for global variable 'end_location'
genSymbols: no visible binding for global variable 'Chromosome'
genSymbols: no visible binding for global variable 'symbol'
transformToLinkInCircle: no visible binding for global variable
  '.circle.x'
transformToLinkInCircle: no visible binding for global variable
  '.circle.y'
transformToLinkInCircle : <anonymous>: no visible binding for global
  variable 'from.x'
transformToLinkInCircle : <anonymous>: no visible binding for global
  variable 'from.y'
transformToLinkInCircle : <anonymous>: no visible binding for global
  variable 'to.x'
transformToLinkInCircle : <anonymous>: no visible binding for global
  variable 'to.y'
mold,ExpressionSet: no visible global function definition for 'exprs'
mold,ExpressionSet: no visible global function definition for 'pData'
mold,RleList: no visible binding for global variable 'xRleList'
mold,eSet: no visible global function definition for 'phenoData'
mold,eSet: no visible global function definition for 'melt'
mold,eSet: no visible global function definition for 'varLabels'
Undefined global functions or variables:
  .circle.x .circle.y Chromosome end_location exprs from.x from.y melt
  pData phenoData start_location symbol to.x to.y varLabels xRleList
* 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 'C:/Users/biocbuild/bbs-3.6-bioc/meat/biovizBase.buildbin-libdir/biovizBase/libs/i386/biovizBase.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
crunch-method 15.88   0.61   35.49
** running examples for arch 'x64' ... OK
Examples with CPU or elapsed time > 5s
              user system elapsed
crunch-method 17.2   0.54   17.73
* checking for unstated dependencies in 'tests' ... OK
* checking tests ...
** running tests for arch 'i386' ...
  Running 'runTests.R'
 OK
** running tests for arch 'x64' ...
  Running 'runTests.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: 4 NOTEs
See
  'C:/Users/biocbuild/bbs-3.6-bioc/meat/biovizBase.Rcheck/00check.log'
for details.


biovizBase.Rcheck/00install.out:


install for i386

* installing *source* package 'biovizBase' ...
** libs
C:/Rtools/mingw_32/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.6-B/R/include" -DNDEBUG     -I"C:/local323/include"     -O3 -Wall  -std=gnu99 -mtune=core2 -c R_init_biovizBase.c -o R_init_biovizBase.o
C:/Rtools/mingw_32/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.6-B/R/include" -DNDEBUG     -I"C:/local323/include"     -O3 -Wall  -std=gnu99 -mtune=core2 -c bin_offsets.c -o bin_offsets.o
bin_offsets.c: In function 'scan_bam_bin_offsets':
bin_offsets.c:57:15: warning: pointer targets in passing argument 1 of 'strncmp' differ in signedness [-Wpointer-sign]
   if (strncmp(b, "BAI\1", 4))
               ^
In file included from C:/Users/BIOCBU˜1/BBS-3˜1.6-B/R/include/R_ext/RS.h:34:0,
                 from C:/Users/BIOCBU˜1/BBS-3˜1.6-B/R/include/Rdefines.h:37,
                 from bin_offsets.h:1,
                 from bin_offsets.c:3:
C:/Rtools/mingw_32/i686-w64-mingw32/include/string.h:76:15: note: expected 'const char *' but argument is of type 'Rbyte *'
   int __cdecl strncmp(const char *_Str1,const char *_Str2,size_t _MaxCount);
               ^
C:/Rtools/mingw_32/bin/gcc -shared -s -static-libgcc -o biovizBase.dll tmp.def R_init_biovizBase.o bin_offsets.o -LC:/local323/lib/i386 -LC:/local323/lib -LC:/Users/BIOCBU˜1/BBS-3˜1.6-B/R/bin/i386 -lR
installing to C:/Users/biocbuild/bbs-3.6-bioc/meat/biovizBase.buildbin-libdir/biovizBase/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 'biovizBase' ...
** libs
C:/Rtools/mingw_64/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.6-B/R/include" -DNDEBUG     -I"C:/local323/include"     -O2 -Wall  -std=gnu99 -mtune=core2 -c R_init_biovizBase.c -o R_init_biovizBase.o
C:/Rtools/mingw_64/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.6-B/R/include" -DNDEBUG     -I"C:/local323/include"     -O2 -Wall  -std=gnu99 -mtune=core2 -c bin_offsets.c -o bin_offsets.o
bin_offsets.c: In function 'scan_bam_bin_offsets':
bin_offsets.c:57:15: warning: pointer targets in passing argument 1 of 'strncmp' differ in signedness [-Wpointer-sign]
   if (strncmp(b, "BAI\1", 4))
               ^
In file included from C:/Users/BIOCBU˜1/BBS-3˜1.6-B/R/include/R_ext/RS.h:34:0,
                 from C:/Users/BIOCBU˜1/BBS-3˜1.6-B/R/include/Rdefines.h:37,
                 from bin_offsets.h:1,
                 from bin_offsets.c:3:
C:/Rtools/mingw_64/x86_64-w64-mingw32/include/string.h:76:15: note: expected 'const char *' but argument is of type 'Rbyte *'
   int __cdecl strncmp(const char *_Str1,const char *_Str2,size_t _MaxCount);
               ^
C:/Rtools/mingw_64/bin/gcc -shared -s -static-libgcc -o biovizBase.dll tmp.def R_init_biovizBase.o bin_offsets.o -LC:/local323/lib/x64 -LC:/local323/lib -LC:/Users/BIOCBU˜1/BBS-3˜1.6-B/R/bin/x64 -lR
installing to C:/Users/biocbuild/bbs-3.6-bioc/meat/biovizBase.buildbin-libdir/biovizBase/libs/x64
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'biovizBase' as biovizBase_1.25.1.zip
* DONE (biovizBase)

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

nameusersystemelapsed
CRC0.010.000.02
GCcontent0.960.111.06
addStepping-method0.730.020.75
aes-utils000
colorBlindSafePal000
containLetters000
crc1.GeRL000
crunch-method15.88 0.6135.49
darned_hg19_subset5000.030.000.03
flatGrl0.170.010.19
genesymbol0.110.000.11
getBioColor000
getFormalNames000
getGaps0.700.030.74
getIdeoGR0.120.020.14
getIdeogram000
hg19Ideogram000
hg19IdeogramCyto0.000.010.02
ideo0.030.020.04
ideoCyto0.050.000.05
isIdeogram0.010.000.02
isMatchedWithModel0.390.010.40
isSimpleIdeogram0.040.020.05
maxGap-method0.210.000.22
pileupAsGRanges000
pileupGRangesAsVariantTable000
plotColorLegend000
scale0.180.020.19
showColor0.010.000.01
shrinkageFun-method0.140.000.14
splitByFacets-method0.300.010.31
strip_formula_dots000
subsetArgsByFormals000
transform1.450.061.52
transformGRangesForEvenSpace0.190.000.19

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

nameusersystemelapsed
CRC0.100.000.09
GCcontent1.720.001.72
addStepping-method1.570.031.59
aes-utils000
colorBlindSafePal000
containLetters000
crc1.GeRL0.010.000.02
crunch-method17.20 0.5417.73
darned_hg19_subset5000.040.000.03
flatGrl0.320.010.35
genesymbol0.080.030.11
getBioColor000
getFormalNames000
getGaps1.050.001.04
getIdeoGR0.190.020.21
getIdeogram000
hg19Ideogram0.010.000.01
hg19IdeogramCyto0.020.000.02
ideo0.040.000.05
ideoCyto0.080.000.07
isIdeogram000
isMatchedWithModel0.550.000.55
isSimpleIdeogram0.030.000.03
maxGap-method0.310.030.35
pileupAsGRanges000
pileupGRangesAsVariantTable000
plotColorLegend0.020.000.01
scale0.260.020.28
showColor000
shrinkageFun-method0.20.00.2
splitByFacets-method0.340.010.36
strip_formula_dots000
subsetArgsByFormals000
transform1.920.051.97
transformGRangesForEvenSpace0.230.010.25