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Package 79/479HostnameOS / ArchBUILDCHECKBUILD BIN
CGEN 1.5.0
William Wheeler
Snapshot Date: 2011-07-06 19:21:50 -0700 (Wed, 06 Jul 2011)
URL: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/CGEN
Last Changed Rev: 54802 / Revision: 56603
Last Changed Date: 2011-04-13 15:36:43 -0700 (Wed, 13 Apr 2011)
wilson2 Linux (openSUSE 11.4) / x86_64  OK [ OK ]
liverpool Windows Server 2003 R2 (32-bit) / x64  OK  OK  OK 
gewurz Windows Server 2008 R2 Enterprise (64-bit) / x64  OK  OK  OK 
moscato1 Windows Server 2008 R2 Enterprise (64-bit) / x64  OK  OK  OK 
pitt Mac OS X Leopard (10.5.8) / i386  OK  OK  OK 

Summary

Package: CGEN
Version: 1.5.0
Command: /home/biocbuild/bbs-2.9-bioc/R/bin/R CMD check --no-vignettes --timings CGEN_1.5.0.tar.gz
StartedAt: 2011-07-06 23:57:04 -0700 (Wed, 06 Jul 2011)
EndedAt: 2011-07-06 23:58:38 -0700 (Wed, 06 Jul 2011)
EllapsedTime: 94.2 seconds
RetCode: 0
Status:  OK 
CheckDir: CGEN.Rcheck
Warnings: 0

Command output

* using log directory ‘/loc/home/biocbuild/bbs-2.9-bioc/meat/CGEN.Rcheck’
* using R version 2.14.0 Under development (unstable) (2011-06-15 r56138)
* using platform: x86_64-unknown-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘CGEN/DESCRIPTION’ ... OK
* this is package ‘CGEN’ version ‘1.5.0’
* checking package name space information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking whether package ‘CGEN’ 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 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 name space can be loaded with stated dependencies ... OK
* checking whether the name space 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 ... 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 ... NOTE
‘library’ or ‘require’ call not declared from: ‘cluster’
* 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 examples ... OK
* checking for unstated dependencies in vignettes ... NOTE
‘library’ or ‘require’ call not declared from: ‘cluster’
* 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

CGEN.Rcheck/00install.out:

* installing *source* package ‘CGEN’ ...
** libs
gcc -std=gnu99 -I/home/biocbuild/bbs-2.9-bioc/R/include  -I/usr/local/include    -fpic  -g -O2 -Wall -c CML.c -o CML.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.9-bioc/R/include  -I/usr/local/include    -fpic  -g -O2 -Wall -c ccl.c -o ccl.o
ccl.c:386:13: warning: ‘tree_print’ defined but not used
gfortran   -fpic  -g -O2 -Wall -c csclust.f -o csclust.o
Warning: Nonconforming tab character in column 1 of line 46
Warning: Nonconforming tab character in column 1 of line 83
Warning: Nonconforming tab character in column 2 of line 190
Warning: Nonconforming tab character in column 1 of line 203
Warning: Nonconforming tab character in column 1 of line 205
Warning: Nonconforming tab character in column 1 of line 207
csclust.f:222.3:

650   RETURN                                                            
   1
Warning: Label 650 at (1) defined but not used
gcc -std=gnu99 -I/home/biocbuild/bbs-2.9-bioc/R/include  -I/usr/local/include    -fpic  -g -O2 -Wall -c fsclust.c -o fsclust.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.9-bioc/R/include  -I/usr/local/include    -fpic  -g -O2 -Wall -c hcl.c -o hcl.o
hcl.c:375:13: warning: ‘tree_print’ defined but not used
gcc -std=gnu99 -I/home/biocbuild/bbs-2.9-bioc/R/include  -I/usr/local/include    -fpic  -g -O2 -Wall -c pmatch.c -o pmatch.o
gcc -std=gnu99 -shared -L/usr/local/lib64 -o CGEN.so CML.o ccl.o csclust.o fsclust.o hcl.o pmatch.o -lgfortran -lm -L/home/biocbuild/bbs-2.9-bioc/R/lib -lR
installing to /loc/home/biocbuild/bbs-2.9-bioc/meat/CGEN.Rcheck/CGEN/libs
** R
** data
** exec
** inst
** preparing package for lazy loading
Loading required package: splines
** help
*** installing help indices
** building package indices ...
*** tangling vignette sources ...
   ‘vignette.Rnw’ 
** testing if installed package can be loaded

* DONE (CGEN)

CGEN.Rcheck/CGEN-Ex.timings:

nameusersystemelapsed
LocusMapData0.0240.0000.026
QQ.plot0.0080.0000.005
SNPdata0.0120.0000.012
Xdata0.0120.0040.015
chromosome.plot0.1600.0040.163
getMatchedSets28.653 0.34029.238
getSummary0.0160.0000.053
getWaldTest0.0080.0000.010
printEffects0.1640.0000.168
recode.geno0.0040.0000.005
snp.effects0.160.000.16
snp.list0.0000.0040.000
snp.logistic0.2600.0000.264
snp.matched21.714 0.00021.770
snp.scan.logistic0.0080.0000.006