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Package 345/609HostnameOS / ArchBUILDCHECKBUILD BIN
LVSmiRNA 1.8.0
Stefano Calza
Snapshot Date: 2013-03-24 16:21:20 -0700 (Sun, 24 Mar 2013)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_2_11/madman/Rpacks/LVSmiRNA
Last Changed Rev: 70050 / Revision: 74773
Last Changed Date: 2012-10-01 15:16:24 -0700 (Mon, 01 Oct 2012)
lamb1 Linux (openSUSE 12.1) / x86_64  OK [ WARNINGS ]
moscato1 Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64  OK  WARNINGS  OK 
perceval Mac OS X Leopard (10.5.8) / i386  OK  WARNINGS  OK 

Summary

Package: LVSmiRNA
Version: 1.8.0
Command: /home/biocbuild/bbs-2.11-bioc/R/bin/R CMD check --no-vignettes --timings LVSmiRNA_1.8.0.tar.gz
StartedAt: 2013-03-25 02:40:36 -0700 (Mon, 25 Mar 2013)
EndedAt: 2013-03-25 02:41:59 -0700 (Mon, 25 Mar 2013)
EllapsedTime: 82.5 seconds
RetCode: 0
Status:  WARNINGS 
CheckDir: LVSmiRNA.Rcheck
Warnings: 1

Command output

* using log directory ‘/loc/home/biocbuild/bbs-2.11-bioc/meat/LVSmiRNA.Rcheck’
* using R version 2.15.3 (2013-03-01)
* using platform: x86_64-unknown-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘LVSmiRNA/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘LVSmiRNA’ version ‘1.8.0’
* checking package namespace information ... OK
* checking package dependencies ... NOTE
Packages which this enhances but not available for checking:
  ‘multicore’ ‘Rmpi’
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking whether package ‘LVSmiRNA’ can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... 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 ... WARNING
Foreign function call with ‘PACKAGE’ argument in a base package:
  .Call("La_dgesv", ..., PACKAGE = "base")
Packages should not make .C/.Call/.Fortran calls to base packages. They
are not part of the API, for use only by R itself and subject to change
without notice.
* 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 ... OK
* checking installed files from ‘inst/doc’ ... OK
* checking examples ... 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 was 1 note.
See
  ‘/loc/home/biocbuild/bbs-2.11-bioc/meat/LVSmiRNA.Rcheck/00check.log’
for details.

LVSmiRNA.Rcheck/00install.out:

* installing *source* package ‘LVSmiRNA’ ...
** libs
gcc -std=gnu99 -I/home/biocbuild/bbs-2.11-bioc/R/include -DNDEBUG  -I/usr/local/include    -fpic  -g -O2  -Wall -c basic_fns.c -o basic_fns.o
basic_fns.c: In function ‘lvs_median’:
basic_fns.c:146:7: warning: unused variable ‘i’ [-Wunused-variable]
gcc -std=gnu99 -I/home/biocbuild/bbs-2.11-bioc/R/include -DNDEBUG  -I/usr/local/include    -fpic  -g -O2  -Wall -c init.c -o init.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.11-bioc/R/include -DNDEBUG  -I/usr/local/include    -fpic  -g -O2  -Wall -c lvs_rlm.c -o lvs_rlm.o
lvs_rlm.c: In function ‘gamma_fit’:
lvs_rlm.c:175:30: warning: variable ‘converged’ set but not used [-Wunused-but-set-variable]
lvs_rlm.c: In function ‘test_gamma_fit’:
lvs_rlm.c:286:30: warning: variable ‘converged’ set but not used [-Wunused-but-set-variable]
gcc -std=gnu99 -shared -L/usr/local/lib64 -o LVSmiRNA.so basic_fns.o init.o lvs_rlm.o -lgfortran -lm -lquadmath -L/home/biocbuild/bbs-2.11-bioc/R/lib -lRlapack -L/home/biocbuild/bbs-2.11-bioc/R/lib -lRblas -L/home/biocbuild/bbs-2.11-bioc/R/lib -lR
installing to /loc/home/biocbuild/bbs-2.11-bioc/meat/LVSmiRNA.Rcheck/LVSmiRNA/libs
** R
** data
** inst
** preparing package for lazy loading
Warning: replacing previous import ‘boxplot’ when loading ‘graphics’
** help
*** installing help indices
** building package indices
** installing vignettes
   ‘LVSmiRNA.Rnw’ 
** testing if installed package can be loaded
Warning: replacing previous import ‘boxplot’ when loading ‘graphics’

* DONE (LVSmiRNA)

LVSmiRNA.Rcheck/LVSmiRNA-Ex.timings:

nameusersystemelapsed
RLM0.0120.0000.011
estVC0.0000.0000.001
lvs000
plotRA000
read.mir000
rlmFit0.0000.0000.001
summarize000