Back to the "Multiple platform build/check report" A  B  C  D  E  F  G  H  I  J  K  L  M  N  O  P  Q  R  S  T  U [V] W  X  Y  Z 

Package 591/609HostnameOS / ArchBUILDCHECKBUILD BIN
VanillaICE 1.20.3
Robert Scharpf
Snapshot Date: 2013-03-24 16:21:20 -0700 (Sun, 24 Mar 2013)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_2_11/madman/Rpacks/VanillaICE
Last Changed Rev: 70360 / Revision: 74773
Last Changed Date: 2012-10-09 15:40:50 -0700 (Tue, 09 Oct 2012)
lamb1 Linux (openSUSE 12.1) / x86_64  OK  WARNINGS 
moscato1 Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64  OK  WARNINGS  OK 
perceval Mac OS X Leopard (10.5.8) / i386  OK [ WARNINGS ] OK 

Summary

Package: VanillaICE
Version: 1.20.3
Command: /Library/Frameworks/R.framework/Versions/2.15/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch VanillaICE_1.20.3.tar.gz
StartedAt: 2013-03-25 01:34:35 -0700 (Mon, 25 Mar 2013)
EndedAt: 2013-03-25 01:41:22 -0700 (Mon, 25 Mar 2013)
EllapsedTime: 406.7 seconds
RetCode: 0
Status:  WARNINGS 
CheckDir: VanillaICE.Rcheck
Warnings: 1

Command output

* using log directory '/Users/biocbuild/bbs-2.11-bioc/meat/VanillaICE.Rcheck'
* using R version 2.15.3 (2013-03-01)
* using platform: i386-apple-darwin9.8.0 (32-bit)
* using session charset: ASCII
* using option '--no-vignettes'
* checking for file 'VanillaICE/DESCRIPTION' ... OK
* this is package 'VanillaICE' version '1.20.3'
* 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 whether package 'VanillaICE' can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... 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
* 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 for unstated 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
gcPercent : gcFunction: no visible global function definition for
  'alphabetFrequency'
hmmBeadStudioSetList: no visible binding for global variable 'i'
hmmOligoSetList: no visible binding for global variable 'i'
hmmOligoSetList: no visible binding for global variable 'rd'
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... WARNING
Undocumented S4 methods:
  generic '[' and siglist 'gSetList,ANY,ANY,ANY'
All user-level objects in a package (including S4 classes and methods)
should have documentation entries.
See the chapter 'Writing R documentation files' in the 'Writing R
Extensions' manual.
* 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 for portable compilation flags in Makevars ... OK
* checking for portable use of $(BLAS_LIBS) and $(LAPACK_LIBS) ... OK
* checking compiled code ... OK
* checking sizes of PDF files under 'inst/doc' ... OK
* checking installed files from 'inst/doc' ... OK
* checking examples ... OK
Examples with CPU or elapsed time > 5s
                user system elapsed
BeadStudioSet 18.727  0.467  19.562
hmm-methods   16.983  2.184  19.340
* checking for unstated dependencies in tests ... OK
* checking tests ...
  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 vignettes ... SKIPPED
* checking PDF version of manual ... OK

WARNING: There was 1 warning.
NOTE: There was 1 note.
See
  '/Users/biocbuild/bbs-2.11-bioc/meat/VanillaICE.Rcheck/00check.log'
for details.

VanillaICE.Rcheck/00install.out:

* installing *source* package 'VanillaICE' ...
** libs
*** arch - i386
gcc -arch i386 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/i386 -DNDEBUG  -I/usr/local/include    -fPIC  -g -O2 -Wall -pedantic  -c rinit.c -o rinit.o
gcc -arch i386 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/i386 -DNDEBUG  -I/usr/local/include    -fPIC  -g -O2 -Wall -pedantic  -c viterbi.c -o viterbi.o
viterbi.c: In function 'viterbi':
viterbi.c:108: warning: unused variable 'tp'
viterbi.c:244:27: warning: "/*" within comment
viterbi.c:257:3: warning: "/*" within comment
viterbi.c: In function 'viterbi2':
viterbi.c:262: warning: unused variable 'tt'
viterbi.c:260: warning: unused variable 'tp'
gcc -arch i386 -std=gnu99 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -single_module -multiply_defined suppress -L/usr/local/lib -o VanillaICE.so rinit.o viterbi.o -lm -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
installing to /Users/biocbuild/bbs-2.11-bioc/meat/VanillaICE.Rcheck/VanillaICE/libs/i386
** R
** data
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
   'VanillaICE.Rnw' 
   'crlmmDownstream.Rnw' 
** testing if installed package can be loaded

* DONE (VanillaICE)

VanillaICE.Rcheck/VanillaICE-Ex.timings:

nameusersystemelapsed
BeadStudioSet18.727 0.46719.562
BeadStudioSetList-methods0.0310.0040.035
BeadStudioSetList0.0220.0030.026
constructOligoSetListFrom2.9570.2243.237
hmm-methods16.983 2.18419.340
hmmResults0.0010.0010.002
icePlatforms000
oligoSetList-methods1.5230.1131.641
read.bsfiles0.7610.0250.786
robustSds0.0820.0110.119