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BioC 3.5: CHECK report for VanillaICE on tokay2

This page was generated on 2017-08-16 13:19:44 -0400 (Wed, 16 Aug 2017).

Package 1354/1382HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
VanillaICE 1.38.0
Robert Scharpf
Snapshot Date: 2017-08-15 17:17:57 -0400 (Tue, 15 Aug 2017)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_3_5/madman/Rpacks/VanillaICE
Last Changed Rev: 129126 / Revision: 131943
Last Changed Date: 2017-04-24 15:25:24 -0400 (Mon, 24 Apr 2017)
malbec2 Linux (Ubuntu 16.04.1 LTS) / x86_64  OK  OK  OK UNNEEDED, same version exists in internal repository
tokay2 Windows Server 2012 R2 Standard / x64  OK  OK [ OK ] OK UNNEEDED, same version exists in internal repository
veracruz2 OS X 10.11.6 El Capitan / x86_64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: VanillaICE
Version: 1.38.0
Command: rm -rf VanillaICE.buildbin-libdir VanillaICE.Rcheck && mkdir VanillaICE.buildbin-libdir VanillaICE.Rcheck && C:\Users\biocbuild\bbs-3.5-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=VanillaICE.buildbin-libdir VanillaICE_1.38.0.tar.gz >VanillaICE.Rcheck\00install.out 2>&1 && cp VanillaICE.Rcheck\00install.out VanillaICE-install.out && C:\Users\biocbuild\bbs-3.5-bioc\R\bin\R.exe CMD check --library=VanillaICE.buildbin-libdir --install="check:VanillaICE-install.out" --force-multiarch --no-vignettes --timings VanillaICE_1.38.0.tar.gz
StartedAt: 2017-08-16 03:27:22 -0400 (Wed, 16 Aug 2017)
EndedAt: 2017-08-16 03:33:57 -0400 (Wed, 16 Aug 2017)
EllapsedTime: 394.2 seconds
RetCode: 0
Status:  OK  
CheckDir: VanillaICE.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   rm -rf VanillaICE.buildbin-libdir VanillaICE.Rcheck && mkdir VanillaICE.buildbin-libdir VanillaICE.Rcheck && C:\Users\biocbuild\bbs-3.5-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=VanillaICE.buildbin-libdir VanillaICE_1.38.0.tar.gz >VanillaICE.Rcheck\00install.out 2>&1 && cp VanillaICE.Rcheck\00install.out VanillaICE-install.out  &&  C:\Users\biocbuild\bbs-3.5-bioc\R\bin\R.exe CMD check --library=VanillaICE.buildbin-libdir --install="check:VanillaICE-install.out" --force-multiarch --no-vignettes --timings VanillaICE_1.38.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'C:/Users/biocbuild/bbs-3.5-bioc/meat/VanillaICE.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 'VanillaICE/DESCRIPTION' ... OK
* this is package 'VanillaICE' version '1.38.0'
* checking package namespace information ... OK
* checking package dependencies ... NOTE
Packages which this enhances but not available for checking:
  'doMC' 'doRedis'
* 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 'VanillaICE' 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
Namespace in Imports field not imported from: 'BSgenome.Hsapiens.UCSC.hg18'
  All declared Imports should be used.
Unexported object imported by a ':::' call: 'SummarizedExperiment:::.ShallowSimpleListAssays0'
  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 ... OK
* 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 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 'C:/Users/biocbuild/bbs-3.5-bioc/meat/VanillaICE.buildbin-libdir/VanillaICE/libs/i386/VanillaICE.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
** running examples for arch 'x64' ... OK
* checking for unstated dependencies in 'tests' ... OK
* checking tests ...
** running tests for arch 'i386' ...
  Running 'doRUnit.R'
 OK
** running tests for arch 'x64' ...
  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: 3 NOTEs
See
  'C:/Users/biocbuild/bbs-3.5-bioc/meat/VanillaICE.Rcheck/00check.log'
for details.


VanillaICE.Rcheck/00install.out:


install for i386

* installing *source* package 'VanillaICE' ...
** libs
C:/Rtools/mingw_32/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG     -I"C:/local323/include"     -O3 -Wall  -std=gnu99 -mtune=core2 -c rinit.c -o rinit.o
C:/Rtools/mingw_32/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG     -I"C:/local323/include"     -O3 -Wall  -std=gnu99 -mtune=core2 -c viterbi.c -o viterbi.o
C:/Rtools/mingw_32/bin/gcc -shared -s -static-libgcc -o VanillaICE.dll tmp.def rinit.o viterbi.o -lm -LC:/local323/lib/i386 -LC:/local323/lib -LC:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/bin/i386 -lR
installing to C:/Users/biocbuild/bbs-3.5-bioc/meat/VanillaICE.buildbin-libdir/VanillaICE/libs/i386
** R
** data
** inst
** preparing package for lazy loading
No methods found in "RSQLite" for requests: dbGetQuery
Creating a new generic function for 'distance' in package 'VanillaICE'
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
No methods found in "RSQLite" for requests: dbGetQuery

install for x64

* installing *source* package 'VanillaICE' ...
** libs
C:/Rtools/mingw_64/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG     -I"C:/local323/include"     -O2 -Wall  -std=gnu99 -mtune=core2 -c rinit.c -o rinit.o
C:/Rtools/mingw_64/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG     -I"C:/local323/include"     -O2 -Wall  -std=gnu99 -mtune=core2 -c viterbi.c -o viterbi.o
C:/Rtools/mingw_64/bin/gcc -shared -s -static-libgcc -o VanillaICE.dll tmp.def rinit.o viterbi.o -lm -LC:/local323/lib/x64 -LC:/local323/lib -LC:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/bin/x64 -lR
installing to C:/Users/biocbuild/bbs-3.5-bioc/meat/VanillaICE.buildbin-libdir/VanillaICE/libs/x64
** testing if installed package can be loaded
No methods found in "RSQLite" for requests: dbGetQuery
* MD5 sums
packaged installation of 'VanillaICE' as VanillaICE_1.38.0.zip
* DONE (VanillaICE)

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

nameusersystemelapsed
ArrayViews-class3.200.163.36
CopyNumScanParams000
EmissionParam-methods0.010.000.02
FilterParam-class0.020.000.01
HMM1.200.031.24
HMMList-class0.570.020.58
HmmParam000
IO000
IdiogramParams-class0.170.060.24
SnpArrayExperiment-class0.160.000.15
SnpExperiment0.050.000.05
SnpGRanges0.120.000.12
TransitionParam000
cnvFilter0.910.010.93
dropDuplicatedMapLocs0.150.000.15
emissionParam0.020.000.02
getExampleSnpExperiment000
getHmmParams0.010.000.01
hmm20.380.000.38
isHeterozygous0.310.030.34
parseSourceFile0.800.020.82
plotting1.230.021.25
robust-statistics000
snpArrayAssays0.000.010.01
sourcePaths000
sweepMode0.190.000.18
threshold000
viewports0.010.000.02

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

nameusersystemelapsed
ArrayViews-class3.590.073.66
CopyNumScanParams000
EmissionParam-methods0.020.000.02
FilterParam-class000
HMM0.700.060.76
HMMList-class0.640.020.66
HmmParam000
IO0.020.000.02
IdiogramParams-class0.230.000.23
SnpArrayExperiment-class0.190.000.19
SnpExperiment0.030.000.03
SnpGRanges0.110.000.11
TransitionParam000
cnvFilter1.170.001.17
dropDuplicatedMapLocs0.270.010.28
emissionParam0.030.000.03
getExampleSnpExperiment000
getHmmParams0.010.000.02
hmm20.530.000.53
isHeterozygous0.270.020.28
parseSourceFile0.660.010.67
plotting1.290.021.32
robust-statistics000
snpArrayAssays0.000.010.01
sourcePaths0.020.000.02
sweepMode0.250.000.25
threshold000
viewports0.020.000.02