LVSmiRNA 1.23.0
Stefano Calza
| Snapshot Date: 2016-09-19 19:15:14 -0700 (Mon, 19 Sep 2016) | | URL: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/LVSmiRNA | | Last Changed Rev: 117081 / Revision: 121152 | | Last Changed Date: 2016-05-03 14:30:44 -0700 (Tue, 03 May 2016) |
| zin1 | Linux (Ubuntu 16.04 LTS) / x86_64 | NotNeeded | OK | [ OK ] | |  |
| moscato1 | Windows Server 2008 R2 Standard (64-bit) / x64 | NotNeeded | OK | OK | OK | |
| morelia | Mac OS X Mavericks (10.9.5) / x86_64 | NotNeeded | OK | OK | OK | |
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### Running command:
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### /home/biocbuild/bbs-3.4-bioc/R/bin/R CMD check --no-vignettes --timings LVSmiRNA_1.23.0.tar.gz
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* using log directory ‘/home/biocbuild/bbs-3.4-bioc/meat/LVSmiRNA.Rcheck’
* using R version 3.3.1 (2016-06-21)
* 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 ‘1.23.0’
* 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 sizes of PDF files under ‘inst/doc’ ... 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-3.4-bioc/meat/LVSmiRNA.Rcheck/00check.log’
for details.
* installing *source* package ‘LVSmiRNA’ ...
** libs
gcc -I/home/biocbuild/bbs-3.4-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-3.4-bioc/R/include -DNDEBUG -I/usr/local/include -fpic -g -O2 -Wall -c init.c -o init.o
gcc -I/home/biocbuild/bbs-3.4-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-3.4-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-3.4-bioc/R/lib -lRlapack -L/home/biocbuild/bbs-3.4-bioc/R/lib -lRblas -L/home/biocbuild/bbs-3.4-bioc/R/lib -lR
installing to /home/biocbuild/bbs-3.4-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)