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Package 98/609HostnameOS / ArchBUILDCHECKBUILD BIN
CGEN 1.10.0
William Wheeler
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/CGEN
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: CGEN
Version: 1.10.0
Command: /home/biocbuild/bbs-2.11-bioc/R/bin/R CMD check --no-vignettes --timings CGEN_1.10.0.tar.gz
StartedAt: 2013-03-24 23:59:29 -0700 (Sun, 24 Mar 2013)
EndedAt: 2013-03-25 00:01:11 -0700 (Mon, 25 Mar 2013)
EllapsedTime: 102.0 seconds
RetCode: 0
Status:  WARNINGS 
CheckDir: CGEN.Rcheck
Warnings: 1

Command output

* using log directory ‘/loc/home/biocbuild/bbs-2.11-bioc/meat/CGEN.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 ‘CGEN/DESCRIPTION’ ... OK
* this is package ‘CGEN’ version ‘1.10.0’
* 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 ‘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 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 ... WARNING
Foreign function call with ‘PACKAGE’ argument in a base package:
  .Fortran("hcass2", ..., PACKAGE = "stats")
Packages should not make .C/.Call/.Fortran calls to base packages. They
are not part of the API, for use only by R itself and subject to change
without notice.
* checking R code for possible problems ... NOTE
snp.scan.logistic : calcEffects: warning in effects.init(temp$parms,
  temp$cov, eff$var1, eff$var2, eff$snp.levels, eff$var.levels, base1 =
  0, base2 = eff$var.base, int.var = eff$int.var, effects = type, sep =
  eff$sep): partial argument match of 'sep' to 'sep1'
* 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 ... NOTE
File ‘/loc/home/biocbuild/bbs-2.11-bioc/meat/CGEN.Rcheck/CGEN/libs/CGEN.so’:
  Found ‘exit’, possibly from ‘exit’ (C)
    Objects: ‘ccl.o’, ‘hcl.o’
  Found ‘printf’, possibly from ‘printf’ (C)
    Object: ‘CML.o’
  Found ‘puts’, possibly from ‘printf’ (C), ‘puts’ (C)
    Objects: ‘CML.o’, ‘ccl.o’, ‘hcl.o’

Compiled code should not call functions which might terminate R nor
write to stdout/stderr instead of to the console.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
* checking installed files from ‘inst/doc’ ... OK
* checking examples ... OK
Examples with CPU or elapsed time > 5s
                 user system elapsed
getMatchedSets 27.973  0.236  28.954
snp.matched    21.602  0.104  22.904
* 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/CGEN.Rcheck/00check.log’
for details.

CGEN.Rcheck/00install.out:

* installing *source* package ‘CGEN’ ...
** libs
gcc -std=gnu99 -I/home/biocbuild/bbs-2.11-bioc/R/include -DNDEBUG  -I/usr/local/include    -fpic  -g -O2  -Wall -c CML.c -o CML.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.11-bioc/R/include -DNDEBUG  -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 [-Wunused-function]
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-2.11-bioc/R/include -DNDEBUG  -I/usr/local/include    -fpic  -g -O2  -Wall -c fsclust.c -o fsclust.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.11-bioc/R/include -DNDEBUG  -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 [-Wunused-function]
gcc -std=gnu99 -I/home/biocbuild/bbs-2.11-bioc/R/include -DNDEBUG  -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 -lquadmath -L/home/biocbuild/bbs-2.11-bioc/R/lib -lR
installing to /loc/home/biocbuild/bbs-2.11-bioc/meat/CGEN.Rcheck/CGEN/libs
** R
** data
** exec
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
   ‘vignette.Rnw’ 
** testing if installed package can be loaded

* DONE (CGEN)

CGEN.Rcheck/CGEN-Ex.timings:

nameusersystemelapsed
LocusMapData0.0200.0080.032
QQ.plot0.0080.0000.008
SNPdata0.0120.0000.014
Xdata0.020.000.02
chromosome.plot0.2160.0000.236
getMatchedSets27.973 0.23628.954
getSummary0.0120.0000.011
getWaldTest0.0080.0000.038
printEffects0.1600.0040.169
recode.geno0.0040.0000.004
snp.effects0.1520.0040.183
snp.list000
snp.logistic0.2600.0040.290
snp.matched21.602 0.10422.904
snp.scan.logistic0.0080.0000.006