gaga 2.5.4
David Rossell
| Snapshot Date: 2013-03-24 17:01:43 -0700 (Sun, 24 Mar 2013) | | URL: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/gaga | | Last Changed Rev: 73920 / Revision: 74774 | | Last Changed Date: 2013-03-05 05:57:43 -0800 (Tue, 05 Mar 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 Leopard (10.5.8) / i386 | OK | WARNINGS | OK |
* using log directory ‘/home/biocbuild/bbs-2.12-bioc/meat/gaga.Rcheck’
* using R version 3.0.0 beta (2013-03-19 r62328)
* using platform: x86_64-unknown-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘gaga/DESCRIPTION’ ... OK
* this is package ‘gaga’ version ‘2.5.4’
* checking package namespace information ... OK
* checking package dependencies ... NOTE
Package which this enhances but not available for checking: ‘multicore’
* 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 ‘gaga’ can be installed ... [23s/24s] OK
* checking installed package size ... OK
* checking package directory ... 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 ... OK
* checking R code for possible problems ... NOTE
adjustfitNN : f: warning in fitNN(xsim, group = "group", B = B, trace =
FALSE): partial argument match of 'group' to 'groups'
* 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 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 ‘/home/biocbuild/bbs-2.12-bioc/meat/gaga.Rcheck/gaga/libs/gaga.so’:
Found ‘exit’, possibly from ‘exit’ (C)
Object: ‘cstat.o’
Found ‘putchar’, possibly from ‘putchar’ (C)
Objects: ‘cseqdesma.o’, ‘cstat.o’
Found ‘puts’, possibly from ‘printf’ (C), ‘puts’ (C)
Objects: ‘cseqdesma.o’, ‘cstat.o’
Found ‘stderr’, possibly from ‘stderr’ (C)
Object: ‘cstat.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 installed files from ‘inst/doc’ ... OK
* checking examples ... [14s/15s] OK
* 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
‘/home/biocbuild/bbs-2.12-bioc/meat/gaga.Rcheck/00check.log’
for details.
* installing *source* package ‘gaga’ ...
** libs
gcc -std=gnu99 -I/home/biocbuild/bbs-2.12-bioc/R/include -DNDEBUG -I/usr/local/include -fpic -g -O2 -Wall -c cseqdesma.c -o cseqdesma.o
cseqdesma.c: In function ‘expected_fp’:
cseqdesma.c:3017:56: warning: variable ‘B10’ set but not used [-Wunused-but-set-variable]
cseqdesma.c: In function ‘utsample_predC’:
cseqdesma.c:4009:88: warning: variable ‘pcum’ set but not used [-Wunused-but-set-variable]
gcc -std=gnu99 -I/home/biocbuild/bbs-2.12-bioc/R/include -DNDEBUG -I/usr/local/include -fpic -g -O2 -Wall -c cstat.c -o cstat.o
cstat.c: In function ‘scanFloat’:
cstat.c:494:3: warning: format not a string literal and no format arguments [-Wformat-security]
cstat.c: In function ‘scanDouble’:
cstat.c:502:3: warning: format not a string literal and no format arguments [-Wformat-security]
cstat.c: In function ‘fscanDouble’:
cstat.c:510:3: warning: format not a string literal and no format arguments [-Wformat-security]
cstat.c: In function ‘scanInt’:
cstat.c:520:3: warning: format not a string literal and no format arguments [-Wformat-security]
cstat.c: In function ‘fscanInt’:
cstat.c:530:3: warning: format not a string literal and no format arguments [-Wformat-security]
cstat.c: In function ‘scanLong’:
cstat.c:541:3: warning: format not a string literal and no format arguments [-Wformat-security]
cstat.c: In function ‘scanArray’:
cstat.c:558:3: warning: format not a string literal and no format arguments [-Wformat-security]
cstat.c: In function ‘scanDoubleArray’:
cstat.c:570:3: warning: format not a string literal and no format arguments [-Wformat-security]
cstat.c: In function ‘scanDoubleMatrix’:
cstat.c:606:3: warning: format not a string literal and no format arguments [-Wformat-security]
cstat.c: In function ‘scanIntArray’:
cstat.c:631:3: warning: format not a string literal and no format arguments [-Wformat-security]
cstat.c:631:9: warning: ignoring return value of ‘fscanf’, declared with attribute warn_unused_result [-Wunused-result]
cstat.c: In function ‘scanDoubleMatrix’:
cstat.c:606:9: warning: ignoring return value of ‘fscanf’, declared with attribute warn_unused_result [-Wunused-result]
cstat.c: In function ‘fscanString’:
cstat.c:599:8: warning: ignoring return value of ‘fgets’, declared with attribute warn_unused_result [-Wunused-result]
cstat.c: In function ‘scanString’:
cstat.c:593:8: warning: ignoring return value of ‘fgets’, declared with attribute warn_unused_result [-Wunused-result]
cstat.c: In function ‘scanDoubleArray’:
cstat.c:570:9: warning: ignoring return value of ‘fscanf’, declared with attribute warn_unused_result [-Wunused-result]
cstat.c: In function ‘scanArray’:
cstat.c:558:9: warning: ignoring return value of ‘fscanf’, declared with attribute warn_unused_result [-Wunused-result]
cstat.c: In function ‘scanLong’:
cstat.c:541:9: warning: ignoring return value of ‘fscanf’, declared with attribute warn_unused_result [-Wunused-result]
cstat.c: In function ‘fscanInt’:
cstat.c:530:9: warning: ignoring return value of ‘fscanf’, declared with attribute warn_unused_result [-Wunused-result]
cstat.c: In function ‘scanInt’:
cstat.c:520:9: warning: ignoring return value of ‘fscanf’, declared with attribute warn_unused_result [-Wunused-result]
cstat.c: In function ‘fscanDouble’:
cstat.c:510:9: warning: ignoring return value of ‘fscanf’, declared with attribute warn_unused_result [-Wunused-result]
cstat.c: In function ‘scanDouble’:
cstat.c:502:9: warning: ignoring return value of ‘fscanf’, declared with attribute warn_unused_result [-Wunused-result]
cstat.c: In function ‘scanFloat’:
cstat.c:494:9: warning: ignoring return value of ‘fscanf’, declared with attribute warn_unused_result [-Wunused-result]
gcc -std=gnu99 -shared -L/usr/local/lib -o gaga.so cseqdesma.o cstat.o -L/home/biocbuild/bbs-2.12-bioc/R/lib -lR
installing to /home/biocbuild/bbs-2.12-bioc/meat/gaga.Rcheck/gaga/libs
** R
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
‘gagamanual.Rnw’
** testing if installed package can be loaded
* DONE (gaga)