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BioC 2.14: CHECK report for CGEN on zin2

This page was generated on 2014-10-08 08:48:51 -0700 (Wed, 08 Oct 2014).

Package 129/824HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
CGEN 2.6.1
William Wheeler
Snapshot Date: 2014-10-07 17:20:37 -0700 (Tue, 07 Oct 2014)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_2_14/madman/Rpacks/CGEN
Last Changed Rev: 90176 / Revision: 95116
Last Changed Date: 2014-05-09 15:54:26 -0700 (Fri, 09 May 2014)
zin2 Linux (Ubuntu 12.04.4 LTS) / x86_64  NotNeeded  OK [ OK ]
moscato2 Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64  NotNeeded  OK  OK  OK 
petty Mac OS X Snow Leopard (10.6.8) / x86_64  NotNeeded  OK  OK  OK 
morelia Mac OS X Mavericks (10.9.5) / x86_64  NotNeeded  OK  OK  OK 

Summary

Package: CGEN
Version: 2.6.1
Command: /home/biocbuild/bbs-2.14-bioc/R/bin/R CMD check --no-vignettes --timings CGEN_2.6.1.tar.gz
StartedAt: 2014-10-07 22:23:52 -0700 (Tue, 07 Oct 2014)
EndedAt: 2014-10-07 22:25:13 -0700 (Tue, 07 Oct 2014)
EllapsedTime: 81.8 seconds
RetCode: 0
Status:  OK 
CheckDir: CGEN.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-2.14-bioc/R/bin/R CMD check --no-vignettes --timings CGEN_2.6.1.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-2.14-bioc/meat/CGEN.Rcheck’
* using R version 3.1.1 (2014-07-10)
* 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 ‘2.6.1’
* 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 for hidden files and directories ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘CGEN’ can be installed ... [3s/4s] OK
* checking installed package size ... OK
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... NOTE
License components with restrictions not permitted:
  GPL-2 + file LICENSE
* 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 loading without being on the library search path ... OK
* checking 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 ... 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 files in ‘vignettes’ ... OK
* checking examples ... [34s/34s] OK
Examples with CPU or elapsed time > 5s
                 user system elapsed
getMatchedSets 15.993  0.164  16.189
snp.matched    15.613  0.000  15.649
* 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

NOTE: There was 1 note.
See
  ‘/home/biocbuild/bbs-2.14-bioc/meat/CGEN.Rcheck/00check.log’
for details.

CGEN.Rcheck/00install.out:

* installing *source* package ‘CGEN’ ...
** libs
gcc -std=gnu99 -I/home/biocbuild/bbs-2.14-bioc/R/include -DNDEBUG  -I/usr/local/include    -fpic  -g -O2  -Wall -c Additive.c -o Additive.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.14-bioc/R/include -DNDEBUG  -I/usr/local/include    -fpic  -g -O2  -Wall -c CML.c -o CML.o
CML.c:1198:13: warning: ‘print_dVec’ defined but not used [-Wunused-function]
gcc -std=gnu99 -I/home/biocbuild/bbs-2.14-bioc/R/include -DNDEBUG  -I/usr/local/include    -fpic  -g -O2  -Wall -c ccl.c -o ccl.o
ccl.c: In function ‘ccl_optim’:
ccl.c:78:2: warning: passing argument 1 of ‘Rf_error’ makes pointer from integer without a cast [enabled by default]
/home/biocbuild/bbs-2.14-bioc/R/include/R_ext/Error.h:33:6: note: expected ‘const char *’ but argument is of type ‘int’
ccl.c: In function ‘factorial’:
ccl.c:478:2: warning: passing argument 1 of ‘Rf_error’ makes pointer from integer without a cast [enabled by default]
/home/biocbuild/bbs-2.14-bioc/R/include/R_ext/Error.h:33:6: note: expected ‘const char *’ but argument is of type ‘int’
ccl.c: At top level:
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
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Warning: Nonconforming tab character in column 1 of line 270
Warning: Nonconforming tab character in column 1 of line 271
Warning: Nonconforming tab character in column 1 of line 275
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Warning: Nonconforming tab character in column 1 of line 282
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Warning: Nonconforming tab character in column 1 of line 287
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Warning: Nonconforming tab character in column 1 of line 290
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Warning: Nonconforming tab character in column 1 of line 292
Warning: Nonconforming tab character in column 1 of line 293
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Warning: Nonconforming tab character in column 1 of line 296
Warning: Nonconforming tab character in column 1 of line 306
Warning: Nonconforming tab character in column 1 of line 307
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Warning: Nonconforming tab character in column 1 of line 310
Warning: Nonconforming tab character in column 1 of line 311
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Warning: Nonconforming tab character in column 1 of line 313
Warning: Nonconforming tab character in column 1 of line 314
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Warning: Nonconforming tab character in column 1 of line 316
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Warning: Nonconforming tab character in column 1 of line 321
Warning: Nonconforming tab character in column 1 of line 329
csclust.f:222.3:

650   RETURN                                                            
   1
Warning: Label 650 at (1) defined but not used
gcc -std=gnu99 -I/home/biocbuild/bbs-2.14-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-2.14-bioc/R/include -DNDEBUG  -I/usr/local/include    -fpic  -g -O2  -Wall -c hcl.c -o hcl.o
hcl.c: In function ‘hcl_optim’:
hcl.c:72:2: warning: passing argument 1 of ‘Rf_error’ makes pointer from integer without a cast [enabled by default]
/home/biocbuild/bbs-2.14-bioc/R/include/R_ext/Error.h:33:6: note: expected ‘const char *’ but argument is of type ‘int’
hcl.c: In function ‘factorial’:
hcl.c:467:2: warning: passing argument 1 of ‘Rf_error’ makes pointer from integer without a cast [enabled by default]
/home/biocbuild/bbs-2.14-bioc/R/include/R_ext/Error.h:33:6: note: expected ‘const char *’ but argument is of type ‘int’
hcl.c: At top level:
hcl.c:375:13: warning: ‘tree_print’ defined but not used [-Wunused-function]
gcc -std=gnu99 -I/home/biocbuild/bbs-2.14-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/lib -o CGEN.so Additive.o CML.o ccl.o csclust.o fsclust.o hcl.o pmatch.o -lgfortran -lm -lquadmath -L/home/biocbuild/bbs-2.14-bioc/R/lib -lR
installing to /home/biocbuild/bbs-2.14-bioc/meat/CGEN.Rcheck/CGEN/libs
** R
** data
** exec
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (CGEN)

CGEN.Rcheck/CGEN-Ex.timings:

nameusersystemelapsed
LocusMapData0.0240.0040.029
QQ.plot0.0040.0000.008
SNPdata0.0120.0000.013
Xdata0.0120.0040.016
additive.test0.6320.0000.635
chromosome.plot0.1120.0040.116
getMatchedSets15.993 0.16416.189
getSummary0.0080.0000.006
getWaldTest0.0040.0040.006
printEffects0.1080.0040.113
recode.geno0.0080.0000.005
snp.effects0.0960.0040.102
snp.effects.plot0.4200.0000.419
snp.list0.0000.0000.001
snp.logistic0.2040.0000.222
snp.matched15.613 0.00015.649
snp.scan.logistic0.0080.0000.006