MEDME 1.30.0
Mattia Pelizzola
| Snapshot Date: 2016-04-22 16:20:12 -0700 (Fri, 22 Apr 2016) | | URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_3_2/madman/Rpacks/MEDME | | Last Changed Rev: 109589 / Revision: 116712 | | Last Changed Date: 2015-10-13 12:36:05 -0700 (Tue, 13 Oct 2015) |
| zin1 | Linux (Ubuntu 14.04.2 LTS) / x86_64 | NotNeeded | OK | [ WARNINGS ] | |  |
| moscato1 | Windows Server 2008 R2 Standard (64-bit) / x64 | NotNeeded | OK | WARNINGS | OK | |
| oaxaca | Mac OS X Mavericks (10.9.5) / x86_64 | NotNeeded | OK | WARNINGS | OK | |
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### Running command:
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### /home/biocbuild/bbs-3.2-bioc/R/bin/R CMD check --no-vignettes --timings MEDME_1.30.0.tar.gz
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* using log directory ‘/home/biocbuild/bbs-3.2-bioc/meat/MEDME.Rcheck’
* using R version 3.2.4 Revised (2016-03-16 r70336)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘MEDME/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘MEDME’ version ‘1.30.0’
* 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 ‘MEDME’ can be installed ... [10s/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
Package in Depends field not imported from: ‘methods’
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
CGcount: no visible binding for global variable ‘Hsapiens’
CGcount: no visible binding for global variable ‘Mmusculus’
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... WARNING
Undocumented S4 methods:
generic '[' and siglist 'MEDMEset,ANY,ANY,ANY'
All user-level objects in a package (including S4 classes and methods)
should have documentation entries.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
* 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 sizes of PDF files under ‘inst/doc’ ... OK
* checking installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... [21s/23s] OK
Examples with CPU or elapsed time > 5s
user system elapsed
CGcount 8.45 0.233 9.298
* 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: 1 WARNING, 3 NOTEs
See
‘/home/biocbuild/bbs-3.2-bioc/meat/MEDME.Rcheck/00check.log’
for details.
* installing *source* package ‘MEDME’ ...
** libs
gcc -std=gnu99 -I/home/biocbuild/bbs-3.2-bioc/R/include -DNDEBUG -I/usr/local/include -fpic -g -O2 -Wall -c MEDMEweight.c -o MEDMEweight.o
MEDMEweight.c: In function ‘MEDMEweight’:
MEDMEweight.c:78:12: warning: ‘weight’ may be used uninitialized in this function [-Wmaybe-uninitialized]
weightSum = weightSum + weight;
^
MEDMEweight.c:91:42: warning: ‘Max’ may be used uninitialized in this function [-Wmaybe-uninitialized]
if(AMSfinal[i] > Max) {AMSfinal[i] = Max;}
^
MEDMEweight.c:92:42: warning: ‘Min’ may be used uninitialized in this function [-Wmaybe-uninitialized]
if(AMSfinal[i] < Min) {AMSfinal[i] = Min;}
^
MEDMEweight.c:90:36: warning: ‘E’ may be used uninitialized in this function [-Wmaybe-uninitialized]
AMSfinal[i] = pow(2, pow( pow(E,B) * (D - Mlim) / (Mlim - C), 1/B));
^
MEDMEweight.c:90:47: warning: ‘D’ may be used uninitialized in this function [-Wmaybe-uninitialized]
AMSfinal[i] = pow(2, pow( pow(E,B) * (D - Mlim) / (Mlim - C), 1/B));
^
MEDMEweight.c:90:63: warning: ‘C’ may be used uninitialized in this function [-Wmaybe-uninitialized]
AMSfinal[i] = pow(2, pow( pow(E,B) * (D - Mlim) / (Mlim - C), 1/B));
^
MEDMEweight.c:90:36: warning: ‘B’ may be used uninitialized in this function [-Wmaybe-uninitialized]
AMSfinal[i] = pow(2, pow( pow(E,B) * (D - Mlim) / (Mlim - C), 1/B));
^
gcc -std=gnu99 -shared -L/home/biocbuild/bbs-3.2-bioc/R/lib -L/usr/local/lib -o MEDME.so MEDMEweight.o -L/home/biocbuild/bbs-3.2-bioc/R/lib -lR
installing to /home/biocbuild/bbs-3.2-bioc/meat/MEDME.Rcheck/MEDME/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 (MEDME)