CGEN 2.4.0
William Wheeler
| Snapshot Date: 2014-04-04 16:20:29 -0700 (Fri, 04 Apr 2014) | | URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_2_13/madman/Rpacks/CGEN | | Last Changed Rev: 81642 / Revision: 88450 | | Last Changed Date: 2013-10-14 14:29:21 -0700 (Mon, 14 Oct 2013) |
| zin1 | Linux (Ubuntu 12.04.4 LTS) / x86_64 | OK | [ OK ] | |
| moscato1 | Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64 | OK | OK | OK |
| perceval | Mac OS X Snow Leopard (10.6.8) / x86_64 | OK | OK | OK |
* using log directory ‘/home/biocbuild/bbs-2.13-bioc/meat/CGEN.Rcheck’
* using R version 3.0.3 (2014-03-06)
* 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 ‘2.4.0’
* 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 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 ... [4s/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 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 for old-style vignette sources ... NOTE
Vignette sources only in ‘inst/doc’:
‘vignette.Rnw’
A ‘vignettes’ directory will be required as from R 3.1.0
* checking examples ... [36s/36s] OK
Examples with CPU or elapsed time > 5s
user system elapsed
getMatchedSets 17.745 0.196 17.983
snp.matched 15.529 0.000 15.555
* 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 were 2 notes.
See
‘/home/biocbuild/bbs-2.13-bioc/meat/CGEN.Rcheck/00check.log’
for details.
* installing *source* package ‘CGEN’ ...
** libs
gcc -std=gnu99 -I/home/biocbuild/bbs-2.13-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-2.13-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-2.13-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-2.13-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-2.13-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
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csclust.f:222.3:
650 RETURN
1
Warning: Label 650 at (1) defined but not used
gcc -std=gnu99 -I/home/biocbuild/bbs-2.13-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-2.13-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-2.13-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-2.13-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-2.13-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-2.13-bioc/R/lib -lR
installing to /home/biocbuild/bbs-2.13-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)