SMAP 1.40.0
Robin Andersson
| Snapshot Date: 2017-08-15 17:17:57 -0400 (Tue, 15 Aug 2017) | | URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_3_5/madman/Rpacks/SMAP | | Last Changed Rev: 129126 / Revision: 131943 | | Last Changed Date: 2017-04-24 15:25:24 -0400 (Mon, 24 Apr 2017) |
| malbec2 | Linux (Ubuntu 16.04.1 LTS) / x86_64 | NotNeeded | OK | [ OK ] | |  |
| tokay2 | Windows Server 2012 R2 Standard / x64 | NotNeeded | OK | OK | OK | |
| veracruz2 | OS X 10.11.6 El Capitan / x86_64 | NotNeeded | OK | OK | OK | |
##############################################################################
##############################################################################
###
### Running command:
###
### /home/biocbuild/bbs-3.5-bioc/R/bin/R CMD check --no-vignettes --timings SMAP_1.40.0.tar.gz
###
##############################################################################
##############################################################################
* using log directory ‘/home/biocbuild/bbs-3.5-bioc/meat/SMAP.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 ‘SMAP/DESCRIPTION’ ... OK
* this is package ‘SMAP’ version ‘1.40.0’
* 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 ‘SMAP’ can be installed ... 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
'library' or 'require' call to ‘methods’ which was already attached by Depends.
Please remove these calls from your code.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
File ‘SMAP/R/AllClasses.R’:
.onLoad calls:
require("methods", quietly = TRUE)
Package startup functions should not change the search path.
See section ‘Good practice’ in '?.onAttach'.
.draw.dist,gaussparam: no visible global function definition for
‘abline’
plot,SMAPObservations-missing: no visible global function definition
for ‘par’
plot,SMAPObservations-missing: no visible global function definition
for ‘points’
plot,SMAPObservations-missing: no visible global function definition
for ‘abline’
plot,SMAPObservations-missing: no visible global function definition
for ‘box’
plot,SMAPObservations-missing: no visible global function definition
for ‘axis’
profilePlot,SMAPProfile: no visible global function definition for
‘par’
profilePlot,SMAPProfile: no visible global function definition for
‘points’
profilePlot,SMAPProfile: no visible global function definition for
‘abline’
profilePlot,SMAPProfile: no visible global function definition for
‘box’
profilePlot,SMAPProfile: no visible global function definition for
‘axis’
profilePlot,SMAPProfiles: no visible global function definition for
‘par’
profilePlot,SMAPProfiles: no visible global function definition for
‘abline’
profilePlot,SMAPProfiles: no visible global function definition for
‘box’
profilePlot,SMAPProfiles: no visible global function definition for
‘axis’
Undefined global functions or variables:
abline axis box par points
Consider adding
importFrom("graphics", "abline", "axis", "box", "par", "points")
to your NAMESPACE file.
* 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 compiled code ... OK
* checking installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU or elapsed time > 5s
user system elapsed
smap 7.396 0.008 7.407
* 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: 3 NOTEs
See
‘/home/biocbuild/bbs-3.5-bioc/meat/SMAP.Rcheck/00check.log’
for details.
* installing *source* package ‘SMAP’ ...
** libs
gcc -I/home/biocbuild/bbs-3.5-bioc/R/include -DNDEBUG -I/usr/local/include -fpic -g -O2 -Wall -c gradient.c -o gradient.o
gradient.c: In function ‘prior_gradient’:
gradient.c:142:7: warning: variable ‘lower’ set but not used [-Wunused-but-set-variable]
int lower;
^
gradient.c: In function ‘hmm_update’:
gradient.c:247:10: warning: unused variable ‘tmp’ [-Wunused-variable]
double tmp;
^
gcc -I/home/biocbuild/bbs-3.5-bioc/R/include -DNDEBUG -I/usr/local/include -fpic -g -O2 -Wall -c init.c -o init.o
gcc -I/home/biocbuild/bbs-3.5-bioc/R/include -DNDEBUG -I/usr/local/include -fpic -g -O2 -Wall -c overlap.c -o overlap.o
gcc -I/home/biocbuild/bbs-3.5-bioc/R/include -DNDEBUG -I/usr/local/include -fpic -g -O2 -Wall -c prob.c -o prob.o
gcc -I/home/biocbuild/bbs-3.5-bioc/R/include -DNDEBUG -I/usr/local/include -fpic -g -O2 -Wall -c viterbi.c -o viterbi.o
gcc -shared -L/home/biocbuild/bbs-3.5-bioc/R/lib -L/usr/local/lib -o SMAP.so gradient.o init.o overlap.o prob.o viterbi.o -L/home/biocbuild/bbs-3.5-bioc/R/lib -lR
installing to /home/biocbuild/bbs-3.5-bioc/meat/SMAP.Rcheck/SMAP/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 (SMAP)