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BioC 3.6: CHECK report for LVSmiRNA on malbec1

This page was generated on 2017-08-16 13:19:06 -0400 (Wed, 16 Aug 2017).

Package 743/1410HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
LVSmiRNA 1.27.0
Stefano Calza
Snapshot Date: 2017-08-15 17:18:21 -0400 (Tue, 15 Aug 2017)
URL: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/LVSmiRNA
Last Changed Rev: 129129 / Revision: 131943
Last Changed Date: 2017-04-24 15:50:57 -0400 (Mon, 24 Apr 2017)
malbec1 Linux (Ubuntu 16.04.1 LTS) / x86_64  NotNeeded  OK [ OK ]UNNEEDED, same version exists in internal repository
tokay1 Windows Server 2012 R2 Standard / x64  NotNeeded  OK  OK  OK UNNEEDED, same version exists in internal repository
veracruz1 OS X 10.11.6 El Capitan / x86_64  NotNeeded  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: LVSmiRNA
Version: 1.27.0
Command: /home/biocbuild/bbs-3.6-bioc/R/bin/R CMD check --no-vignettes --timings LVSmiRNA_1.27.0.tar.gz
StartedAt: 2017-08-16 00:22:16 -0400 (Wed, 16 Aug 2017)
EndedAt: 2017-08-16 00:23:52 -0400 (Wed, 16 Aug 2017)
EllapsedTime: 95.5 seconds
RetCode: 0
Status:  OK 
CheckDir: LVSmiRNA.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.6-bioc/R/bin/R CMD check --no-vignettes --timings LVSmiRNA_1.27.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.6-bioc/meat/LVSmiRNA.Rcheck’
* using R version 3.4.1 (2017-06-30)
* using platform: x86_64-pc-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 ‘1.27.0’
* 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 ‘LVSmiRNA’ can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking ‘build’ 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 loading without being on the library search path ... OK
* checking dependencies in R code ... NOTE
Package in Depends field not imported from: ‘splines’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
Unexported object imported by a ':::' call: ‘vsn:::vsn2trsf’
  See the note in ?`:::` about the use of this operator.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
read.mir: no visible global function definition for ‘read.maimages’
Undefined global functions or variables:
  read.maimages
* 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 ... OK
* checking for GNU extensions in Makefiles ... OK
* checking for portable use of $(BLAS_LIBS) and $(LAPACK_LIBS) ... OK
* checking compiled code ... OK
* checking installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... 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 vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE

Status: 2 NOTEs
See
  ‘/home/biocbuild/bbs-3.6-bioc/meat/LVSmiRNA.Rcheck/00check.log’
for details.


LVSmiRNA.Rcheck/00install.out:

* installing *source* package ‘LVSmiRNA’ ...
** libs
gcc -I/home/biocbuild/bbs-3.6-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]
   int i;
       ^
gcc -I/home/biocbuild/bbs-3.6-bioc/R/include -DNDEBUG   -I/usr/local/include   -fpic  -g -O2  -Wall -c init.c -o init.o
gcc -I/home/biocbuild/bbs-3.6-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]
   int i,j, rows, cols, iter, converged=0;
                              ^
lvs_rlm.c: In function ‘test_gamma_fit’:
lvs_rlm.c:286:30: warning: variable ‘converged’ set but not used [-Wunused-but-set-variable]
   int i,j, rows, cols, iter, converged=0;
                              ^
gcc -shared -L/home/biocbuild/bbs-3.6-bioc/R/lib -L/usr/local/lib -o LVSmiRNA.so basic_fns.o init.o lvs_rlm.o -lgfortran -lm -lquadmath -L/home/biocbuild/bbs-3.6-bioc/R/lib -lRlapack -L/home/biocbuild/bbs-3.6-bioc/R/lib -lRblas -L/home/biocbuild/bbs-3.6-bioc/R/lib -lR
installing to /home/biocbuild/bbs-3.6-bioc/meat/LVSmiRNA.Rcheck/LVSmiRNA/libs
** R
** data
** inst
** preparing package for lazy loading
No methods found in "BiocGenerics" for requests: as.vector, unlist
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
No methods found in "BiocGenerics" for requests: as.vector, unlist
* DONE (LVSmiRNA)

LVSmiRNA.Rcheck/LVSmiRNA-Ex.timings:

nameusersystemelapsed
RLM0.0120.0000.010
estVC0.0040.0000.001
lvs000
plotRA000
read.mir000
rlmFit0.0480.0000.048
summarize0.0000.0000.001