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BioC 2.12: CHECK report for iBMQ on george2

This page was generated on 2013-10-09 09:37:58 -0700 (Wed, 09 Oct 2013).

Package 330/671HostnameOS / ArchBUILDCHECKBUILD BIN
iBMQ 1.0.1
Marie-Pier Scott-Boyer
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/iBMQ
Last Changed Rev: 75531 / Revision: 81334
Last Changed Date: 2013-04-10 13:41:32 -0700 (Wed, 10 Apr 2013)
george2 Linux (Ubuntu 12.04.1 LTS) / x86_64  OK [ OK ]
moscato2 Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64 N O T   S U P P O R T E D
petty Mac OS X Snow Leopard (10.6.8) / x86_64  OK  OK  OK 

Summary

Package: iBMQ
Version: 1.0.1
Command: /home/biocbuild/bbs-2.12-bioc/R/bin/R CMD check --no-vignettes --timings iBMQ_1.0.1.tar.gz
StartedAt: 2013-10-09 02:38:45 -0700 (Wed, 09 Oct 2013)
EndedAt: 2013-10-09 02:39:58 -0700 (Wed, 09 Oct 2013)
EllapsedTime: 73.0 seconds
RetCode: 0
Status:  OK 
CheckDir: iBMQ.Rcheck
Warnings: 0

Command output

* using log directory ‘/home/biocbuild/bbs-2.12-bioc/meat/iBMQ.Rcheck’
* using R version 3.0.1 (2013-05-16)
* using platform: x86_64-unknown-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘iBMQ/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘iBMQ’ version ‘1.0.1’
* 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 ... NOTE
Found the following hidden files and directories:
  .BBSoptions
These were most likely included in error. See section ‘Package
structure’ in the ‘Writing R Extensions’ manual.
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘iBMQ’ can be installed ... [9s/10s] 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 ... 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 compilation flags in Makevars ... OK
* checking for portable use of $(BLAS_LIBS) and $(LAPACK_LIBS) ... OK
* checking compiled code ... NOTE
File ‘/home/biocbuild/bbs-2.12-bioc/meat/iBMQ.Rcheck/iBMQ/libs/iBMQ.so’:
  Found non-API call to R: ‘R_CStackLimit’

Compiled code should not call non-API entry points in R.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
* checking installed files from ‘inst/doc’ ... OK
* checking examples ... [14s/14s] OK
Examples with CPU or elapsed time > 5s
                user system elapsed
eqtlClassifier 7.108  0.052   7.177
* 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

NOTE: There were 2 notes.
See
  ‘/home/biocbuild/bbs-2.12-bioc/meat/iBMQ.Rcheck/00check.log’
for details.

iBMQ.Rcheck/00install.out:

* installing *source* package ‘iBMQ’ ...
checking for gcc... gcc -std=gnu99
checking for C compiler default output file name... a.out
checking whether the C compiler works... yes
checking whether we are cross compiling... no
checking for suffix of executables... 
checking for suffix of object files... o
checking whether we are using the GNU C compiler... yes
checking whether gcc -std=gnu99 accepts -g... yes
checking for gcc -std=gnu99 option to accept ISO C89... none needed
checking how to run the C preprocessor... gcc -std=gnu99 -E
checking for pkg-config... /usr/bin/pkg-config
checking pkg-config is at least version 0.9.0... yes
checking for GSL... yes
checking for grep that handles long lines and -e... /bin/grep
checking for egrep... /bin/grep -E
checking for ANSI C header files... yes
checking for sys/types.h... yes
checking for sys/stat.h... yes
checking for stdlib.h... yes
checking for string.h... yes
checking for memory.h... yes
checking for strings.h... yes
checking for inttypes.h... yes
checking for stdint.h... yes
checking for unistd.h... yes
checking omp.h usability... yes
checking omp.h presence... yes
checking for omp.h... yes
configure: creating ./config.status
config.status: creating src/Makevars
** libs
gcc -std=gnu99 -I/home/biocbuild/bbs-2.12-bioc/R/include -DNDEBUG  -I/usr/local/include   -fopenmp -fpic  -g -O2  -Wall -c ARS.c -o ARS.o
ARS.c: In function ‘sample_conditional’:
ARS.c:64:6: warning: unused variable ‘accept’ [-Wunused-variable]
ARS.c: In function ‘sample_hull’:
ARS.c:424:15: warning: unused variable ‘z_j’ [-Wunused-variable]
ARS.c:405:9: warning: unused variable ‘a’ [-Wunused-variable]
ARS.c:404:9: warning: unused variable ‘R’ [-Wunused-variable]
ARS.c: In function ‘initialize_hull’:
ARS.c:460:9: warning: unused variable ‘tmp’ [-Wunused-variable]
gcc -std=gnu99 -I/home/biocbuild/bbs-2.12-bioc/R/include -DNDEBUG  -I/usr/local/include   -fopenmp -fpic  -g -O2  -Wall -c RngStream.c -o RngStream.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.12-bioc/R/include -DNDEBUG  -I/usr/local/include   -fopenmp -fpic  -g -O2  -Wall -c iBMQ_common.c -o iBMQ_common.o
iBMQ_common.c: In function ‘initialize_parms’:
iBMQ_common.c:376:4: warning: suggest parentheses around comparison in operand of ‘&’ [-Wparentheses]
gcc -std=gnu99 -I/home/biocbuild/bbs-2.12-bioc/R/include -DNDEBUG  -I/usr/local/include   -fopenmp -fpic  -g -O2  -Wall -c main_parallel_sparse.c -o main_parallel_sparse.o
main_parallel_sparse.c: In function ‘update_gene_g’:
main_parallel_sparse.c:299:26: warning: unused variable ‘w_jg’ [-Wunused-variable]
main_parallel_sparse.c:299:22: warning: unused variable ‘p1’ [-Wunused-variable]
main_parallel_sparse.c: In function ‘iBMQ_main’:
main_parallel_sparse.c:278:9: warning: ‘Cfile’ may be used uninitialized in this function [-Wuninitialized]
main_parallel_sparse.c:277:9: warning: ‘Sig2file’ may be used uninitialized in this function [-Wuninitialized]
main_parallel_sparse.c:276:9: warning: ‘Mufile’ may be used uninitialized in this function [-Wuninitialized]
main_parallel_sparse.c:274:9: warning: ‘Bfile’ may be used uninitialized in this function [-Wuninitialized]
main_parallel_sparse.c:273:9: warning: ‘Afile’ may be used uninitialized in this function [-Wuninitialized]
main_parallel_sparse.c:275:9: warning: ‘Pfile’ may be used uninitialized in this function [-Wuninitialized]
gcc -std=gnu99 -I/home/biocbuild/bbs-2.12-bioc/R/include -DNDEBUG  -I/usr/local/include   -fopenmp -fpic  -g -O2  -Wall -c main_parallel_sparse_constC.c -o main_parallel_sparse_constC.o
main_parallel_sparse_constC.c: In function ‘c_qtl_main_parallel_sparse_constC’:
main_parallel_sparse_constC.c:154:19: warning: unused variable ‘Bstart’ [-Wunused-variable]
main_parallel_sparse_constC.c:154:10: warning: unused variable ‘Astart’ [-Wunused-variable]
gcc -std=gnu99 -I/home/biocbuild/bbs-2.12-bioc/R/include -DNDEBUG  -I/usr/local/include   -fopenmp -fpic  -g -O2  -Wall -c norm_gamma_generation.c -o norm_gamma_generation.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.12-bioc/R/include -DNDEBUG  -I/usr/local/include   -fopenmp -fpic  -g -O2  -Wall -c sparse.c -o sparse.o
sparse.c: In function ‘initializeChunk’:
sparse.c:39:27: warning: unused variable ‘tmp’ [-Wunused-variable]
sparse.c:39:21: warning: unused variable ‘last’ [-Wunused-variable]
sparse.c: In function ‘SV_add_el’:
sparse.c:273:6: warning: variable ‘temp_ind’ set but not used [-Wunused-but-set-variable]
gcc -std=gnu99 -shared -L/usr/local/lib -o iBMQ.so ARS.o RngStream.o iBMQ_common.o main_parallel_sparse.o main_parallel_sparse_constC.o norm_gamma_generation.o sparse.o -lgsl -lgslcblas -lm -lgomp -L/home/biocbuild/bbs-2.12-bioc/R/lib -lR
installing to /home/biocbuild/bbs-2.12-bioc/meat/iBMQ.Rcheck/iBMQ/libs
** R
** data
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (iBMQ)

iBMQ.Rcheck/iBMQ-Ex.timings:

nameusersystemelapsed
PPA.liver0.4080.0240.437
calculateThreshold1.3400.0521.440
eqtlClassifier7.1080.0527.177
eqtlFinder1.1680.0321.212
eqtlMcmc0.0840.0080.090
gene0.0960.0000.095
genepos0.0120.0000.011
genotype.liver0.0200.0000.019
hotspotFinder1.0160.0681.087
map.liver0.0080.0000.009
phenotype.liver0.0720.0040.078
probe.liver0.0240.0000.023
snp0.0320.0000.030
snppos0.0200.0000.018