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BioC 3.2: CHECK report for iBMQ on perceval

This page was generated on 2015-10-27 17:35:22 -0400 (Tue, 27 Oct 2015).

Package 512/1104HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
iBMQ 1.10.0
Greg Imholte
Snapshot Date: 2015-10-26 19:24:07 -0400 (Mon, 26 Oct 2015)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_3_2/madman/Rpacks/iBMQ
Last Changed Rev: 109589 / Revision: 109947
Last Changed Date: 2015-10-13 15:36:05 -0400 (Tue, 13 Oct 2015)
linux1.bioconductor.org Linux (Ubuntu 14.04.2 LTS) / x86_64  NotNeeded  OK  OK UNNEEDED, same version exists in internal repository
windows1.bioconductor.org Windows Server 2012 R2 Enterprise SP1 (64-bit) / x64  NotNeeded  OK  OK  OK UNNEEDED, same version exists in internal repository
perceval Mac OS X Snow Leopard (10.6.8) / x86_64  NotNeeded  OK [ OK ] OK UNNEEDED, same version exists in internal repository
oaxaca Mac OS X Mavericks (10.9.5) / x86_64  NotNeeded  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: iBMQ
Version: 1.10.0
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings iBMQ_1.10.0.tar.gz
StartedAt: 2015-10-27 08:58:50 -0400 (Tue, 27 Oct 2015)
EndedAt: 2015-10-27 08:59:53 -0400 (Tue, 27 Oct 2015)
EllapsedTime: 63.3 seconds
RetCode: 0
Status:  OK 
CheckDir: iBMQ.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings iBMQ_1.10.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.2-bioc/meat/iBMQ.Rcheck’
* using R version 3.2.2 Patched (2015-10-08 r69496)
* using platform: x86_64-apple-darwin10.8.0 (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 ‘1.10.0’
* 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 ‘iBMQ’ can be installed ... [7s/11s] OK
* checking installed package size ... OK
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... NOTE
Malformed Description field: should contain one or more complete sentences.
* 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 ... NOTE
Packages in Depends field not imported from:
  ‘Biobase’ ‘ggplot2’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
eqtlMcmc: no visible global function definition for ‘exprs’
* 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 compilation flags in Makevars ... NOTE
Package has both ‘src/Makevars.in’ and ‘src/Makevars’.
Installation with --no-configure' is unlikely to work.  If you intended
‘src/Makevars’ to be used on Windows, rename it to ‘src/Makevars.win’
otherwise remove it.  If ‘configure’ created ‘src/Makevars’, you need a
‘cleanup’ script.
* checking for GNU extensions in Makefiles ... OK
* checking for portable use of $(BLAS_LIBS) and $(LAPACK_LIBS) ... OK
* checking compiled code ... NOTE
File ‘iBMQ/libs/iBMQ.so’:
  Found ‘_printf’, possibly from ‘printf’ (C)
    Object: ‘RngStream.o’

Compiled code should not call entry points which might terminate R nor
write to stdout/stderr instead of to the console, nor the system RNG.

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 files in ‘vignettes’ ... OK
* checking examples ... [11s/11s] OK
Examples with CPU or elapsed time > 5s
                user system elapsed
eqtlClassifier 6.228   0.11   6.338
* 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
* DONE

Status: 5 NOTEs
See
  ‘/Users/biocbuild/bbs-3.2-bioc/meat/iBMQ.Rcheck/00check.log’
for details.


iBMQ.Rcheck/00install.out:

* installing *source* package ‘iBMQ’ ...
checking for gcc... llvm-gcc-4.2 -arch x86_64 -std=gnu99
checking whether the C compiler works... yes
checking for C compiler default output file name... a.out
checking for suffix of executables... 
checking whether we are cross compiling... no
checking for suffix of object files... o
checking whether we are using the GNU C compiler... yes
checking whether llvm-gcc-4.2 -arch x86_64 -std=gnu99 accepts -g... yes
checking for llvm-gcc-4.2 -arch x86_64 -std=gnu99 option to accept ISO C89... none needed
checking how to run the C preprocessor... llvm-gcc-4.2 -arch x86_64 -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... /usr/bin/grep
checking for egrep... /usr/bin/grep -E
checking for ANSI C header files... rm: conftest.dSYM: is a directory
rm: conftest.dSYM: is a directory
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
llvm-gcc-4.2 -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include   -fopenmp -fPIC  -mtune=core2 -g -O2 -Wall  -c ARS.c -o ARS.o
llvm-gcc-4.2 -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include   -fopenmp -fPIC  -mtune=core2 -g -O2 -Wall  -c RngStream.c -o RngStream.o
llvm-gcc-4.2 -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include   -fopenmp -fPIC  -mtune=core2 -g -O2 -Wall  -c iBMQ_common.c -o iBMQ_common.o
llvm-gcc-4.2 -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include   -fopenmp -fPIC  -mtune=core2 -g -O2 -Wall  -c main_parallel_sparse.c -o main_parallel_sparse.o
llvm-gcc-4.2 -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include   -fopenmp -fPIC  -mtune=core2 -g -O2 -Wall  -c main_parallel_sparse_constC.c -o main_parallel_sparse_constC.o
llvm-gcc-4.2 -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include   -fopenmp -fPIC  -mtune=core2 -g -O2 -Wall  -c norm_gamma_generation.c -o norm_gamma_generation.o
llvm-gcc-4.2 -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include   -fopenmp -fPIC  -mtune=core2 -g -O2 -Wall  -c sparse.c -o sparse.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/Library/Frameworks/R.framework/Resources/lib -L/usr/local/lib -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 -L/usr/local/lib -lgsl -lgslcblas -lm -lgomp -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
installing to /Users/biocbuild/bbs-3.2-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.liver0.2620.0240.287
calculateThreshold0.6220.0360.656
eqtlClassifier6.2280.1106.338
eqtlFinder0.6210.0390.659
eqtlMcmc0.0770.0150.092
gene0.0560.0020.059
genepos0.0040.0110.014
genotype.liver0.0080.0010.008
hotspotFinder0.6370.0570.693
map.liver0.0020.0000.002
phenotype.liver0.0660.0110.077
probe.liver0.0170.0110.027
snp0.0150.0100.025
snppos0.0050.0110.015