CGEN 2.2.0
William Wheeler
| Snapshot Date: 2013-10-08 17:00:48 -0700 (Tue, 08 Oct 2013) | | URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_2_12/madman/Rpacks/CGEN | | Last Changed Rev: 75263 / Revision: 81334 | | Last Changed Date: 2013-04-03 14:32:27 -0700 (Wed, 03 Apr 2013) |
| george2 | Linux (Ubuntu 12.04.1 LTS) / x86_64 | OK | WARNINGS | |
| moscato2 | Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64 | OK | OK | OK |
| petty | Mac OS X Snow Leopard (10.6.8) / x86_64 | OK | [ WARNINGS ] | OK |
* using log directory '/Users/biocbuild/bbs-2.12-bioc/meat/CGEN.Rcheck'
* using R version 3.0.1 (2013-05-16)
* using platform: x86_64-apple-darwin10.8.0 (64-bit)
* using session charset: ASCII
* using option '--no-vignettes'
* checking for file 'CGEN/DESCRIPTION' ... OK
* this is package 'CGEN' version '2.2.0'
* 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 ... [7s/7s] OK
* checking installed package size ... OK
* checking package directory ... OK
* checking DESCRIPTION meta-information ... NOTE
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 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 ... 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 ... WARNING
File '/Users/biocbuild/bbs-2.12-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)
Objects: 'Additive.o', 'CML.o'
Found '_puts', possibly from 'printf' (C), 'puts' (C)
Objects: 'Additive.o', 'CML.o', 'ccl.o', 'hcl.o'
Compiled code should not call entry points 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 sizes of PDF files under 'inst/doc' ... OK
* checking installed files from 'inst/doc' ... OK
* checking examples ... [88s/90s] OK
Examples with CPU or elapsed time > 5s
user system elapsed
getMatchedSets 43.095 0.853 44.672
snp.matched 39.046 0.117 39.578
* 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 was 1 note.
See
'/Users/biocbuild/bbs-2.12-bioc/meat/CGEN.Rcheck/00check.log'
for details.
* installing *source* package 'CGEN' ...
** libs
llvm-gcc-4.2 -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/usr/local/include -fPIC -mtune=core2 -g -O2 -c Additive.c -o Additive.o
llvm-gcc-4.2 -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/usr/local/include -fPIC -mtune=core2 -g -O2 -c CML.c -o CML.o
llvm-gcc-4.2 -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/usr/local/include -fPIC -mtune=core2 -g -O2 -c ccl.c -o ccl.o
gfortran-4.2 -arch x86_64 -fPIC -g -O2 -Wall -pedantic -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 1 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
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
Warning: Nonconforming tab character in column 1 of line 276
Warning: Nonconforming tab character in column 1 of line 277
Warning: Nonconforming tab character in column 1 of line 278
Warning: Nonconforming tab character in column 1 of line 282
Warning: Nonconforming tab character in column 1 of line 283
Warning: Nonconforming tab character in column 1 of line 286
Warning: Nonconforming tab character in column 1 of line 287
Warning: Nonconforming tab character in column 1 of line 288
Warning: Nonconforming tab character in column 1 of line 289
Warning: Nonconforming tab character in column 1 of line 290
Warning: Nonconforming tab character in column 1 of line 291
Warning: Nonconforming tab character in column 1 of line 292
Warning: Nonconforming tab character in column 1 of line 293
Warning: Nonconforming tab character in column 1 of line 294
Warning: Nonconforming tab character in column 1 of line 295
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
Warning: Nonconforming tab character in column 1 of line 309
Warning: Nonconforming tab character in column 1 of line 310
Warning: Nonconforming tab character in column 1 of line 311
Warning: Nonconforming tab character in column 1 of line 312
Warning: Nonconforming tab character in column 1 of line 313
Warning: Nonconforming tab character in column 1 of line 314
Warning: Nonconforming tab character in column 1 of line 315
Warning: Nonconforming tab character in column 1 of line 316
Warning: Nonconforming tab character in column 1 of line 317
Warning: Nonconforming tab character in column 1 of line 319
Warning: Nonconforming tab character in column 1 of line 320
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
llvm-gcc-4.2 -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/usr/local/include -fPIC -mtune=core2 -g -O2 -c fsclust.c -o fsclust.o
llvm-gcc-4.2 -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/usr/local/include -fPIC -mtune=core2 -g -O2 -c hcl.c -o hcl.o
llvm-gcc-4.2 -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/usr/local/include -fPIC -mtune=core2 -g -O2 -c pmatch.c -o pmatch.o
llvm-gcc-4.2 -arch x86_64 -std=gnu99 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -single_module -multiply_defined suppress -L/usr/local/lib -L/usr/local/lib -o CGEN.so Additive.o CML.o ccl.o csclust.o fsclust.o hcl.o pmatch.o -L/usr/local/lib/gcc/i686-apple-darwin8/4.2.3/x86_64 -L/usr/local/lib/x86_64 -L/usr/local/lib/gcc/i686-apple-darwin8/4.2.3 -lgfortran -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
installing to /Users/biocbuild/bbs-2.12-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)