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Package 225/609HostnameOS / ArchBUILDCHECKBUILD BIN
gcrma 2.30.0
Z. Wu
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/gcrma
Last Changed Rev: 70050 / Revision: 74773
Last Changed Date: 2012-10-01 15:16:24 -0700 (Mon, 01 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: gcrma
Version: 2.30.0
Command: /home/biocbuild/bbs-2.11-bioc/R/bin/R CMD check --no-vignettes --timings gcrma_2.30.0.tar.gz
StartedAt: 2013-03-25 01:15:02 -0700 (Mon, 25 Mar 2013)
EndedAt: 2013-03-25 01:19:01 -0700 (Mon, 25 Mar 2013)
EllapsedTime: 239.1 seconds
RetCode: 0
Status:  WARNINGS 
CheckDir: gcrma.Rcheck
Warnings: 1

Command output

* using log directory ‘/loc/home/biocbuild/bbs-2.11-bioc/meat/gcrma.Rcheck’
* using R version 2.15.3 (2013-03-01)
* using platform: x86_64-unknown-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘gcrma/DESCRIPTION’ ... OK
* this is package ‘gcrma’ version ‘2.30.0’
* 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 ‘gcrma’ can be installed ... WARNING
Found the following significant warnings:
  /home/biocbuild/bbs-2.11-bioc/R/include/R_ext/RConverters.h:32:2: warning: #warning "R_ext/RConverters.h was deprecated in R 2.15.1 and will be removed in R 3.0.0" [-Wcpp]
See ‘/loc/home/biocbuild/bbs-2.11-bioc/meat/gcrma.Rcheck/00install.out’ for details.
* 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 ... NOTE
Foreign function call with ‘PACKAGE’ argument in a different package:
  .Call("rma_c_complete", ..., PACKAGE = "affy")
See the chapter ‘System and foreign language interfaces’ of the
‘Writing R Extensions’ manual.
* checking R code for possible problems ... NOTE
compute.affinities: no visible binding for global variable
  ‘affinity.spline.coefs’
compute.affinities.nomm: no visible binding for global variable
  ‘affinity.spline.coefs’
compute.affinities2: no visible binding for global variable
  ‘affinity.spline.coefs’
* 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 for portable use of $(BLAS_LIBS) and $(LAPACK_LIBS) ... OK
* checking compiled code ... OK
* checking installed files from ‘inst/doc’ ... OK
* checking examples ... OK
Examples with CPU or elapsed time > 5s
                  user system elapsed
bg.adjust.gcrma 58.864  0.512  60.368
gcrma           44.806  0.240  46.754
* 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 were 2 notes.
See
  ‘/loc/home/biocbuild/bbs-2.11-bioc/meat/gcrma.Rcheck/00check.log’
for details.

gcrma.Rcheck/00install.out:

* installing *source* package ‘gcrma’ ...
** libs
gcc -std=gnu99 -I/home/biocbuild/bbs-2.11-bioc/R/include -DNDEBUG  -I/usr/local/include    -fpic  -g -O2  -Wall -c baseProfile.c -o baseProfile.o
In file included from baseProfile.c:4:0:
/home/biocbuild/bbs-2.11-bioc/R/include/R_ext/RConverters.h:32:2: warning: #warning "R_ext/RConverters.h was deprecated in R 2.15.1 and will be removed in R 3.0.0" [-Wcpp]
gcc -std=gnu99 -I/home/biocbuild/bbs-2.11-bioc/R/include -DNDEBUG  -I/usr/local/include    -fpic  -g -O2  -Wall -c computeAffinities.c -o computeAffinities.o
In file included from computeAffinities.c:3:0:
/home/biocbuild/bbs-2.11-bioc/R/include/R_ext/RConverters.h:32:2: warning: #warning "R_ext/RConverters.h was deprecated in R 2.15.1 and will be removed in R 3.0.0" [-Wcpp]
gcc -std=gnu99 -I/home/biocbuild/bbs-2.11-bioc/R/include -DNDEBUG  -I/usr/local/include    -fpic  -g -O2  -Wall -c postmean.c -o postmean.o
gcc -std=gnu99 -shared -L/usr/local/lib64 -o gcrma.so baseProfile.o computeAffinities.o postmean.o -L/home/biocbuild/bbs-2.11-bioc/R/lib -lR
installing to /loc/home/biocbuild/bbs-2.11-bioc/meat/gcrma.Rcheck/gcrma/libs
** R
** data
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
   ‘gcrma2.0.Rnw’ 
** testing if installed package can be loaded

* DONE (gcrma)

gcrma.Rcheck/gcrma-Ex.timings:

nameusersystemelapsed
bg.adjust.gcrma58.864 0.51260.368
gcrma44.806 0.24046.754