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BioC 3.6: CHECK report for MANOR on malbec1

This page was generated on 2017-08-16 13:17:28 -0400 (Wed, 16 Aug 2017).

Package 756/1410HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
MANOR 1.49.0
Pierre Neuvial
Snapshot Date: 2017-08-15 17:18:21 -0400 (Tue, 15 Aug 2017)
URL: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/MANOR
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: MANOR
Version: 1.49.0
Command: /home/biocbuild/bbs-3.6-bioc/R/bin/R CMD check --no-vignettes --timings MANOR_1.49.0.tar.gz
StartedAt: 2017-08-16 00:25:48 -0400 (Wed, 16 Aug 2017)
EndedAt: 2017-08-16 00:26:19 -0400 (Wed, 16 Aug 2017)
EllapsedTime: 31.0 seconds
RetCode: 0
Status:  OK 
CheckDir: MANOR.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.6-bioc/R/bin/R CMD check --no-vignettes --timings MANOR_1.49.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.6-bioc/meat/MANOR.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 ‘MANOR/DESCRIPTION’ ... OK
* this is package ‘MANOR’ version ‘1.49.0’
* 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 ‘MANOR’ can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... NOTE
Package listed in more than one of Depends, Imports, Suggests, Enhances:
  ‘GLAD’
A package should be listed in only one of these fields.
* 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 ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* 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 compiled code ... NOTE
File ‘MANOR/libs/MANOR.so’:
  Found ‘rand’, possibly from ‘rand’ (C)
    Object: ‘nem_rnd.o’
  Found ‘srand’, possibly from ‘srand’ (C)
    Objects: ‘Rnem_exe.o’, ‘nem_rnd.o’

Compiled code should not call entry points which might terminate R nor
write to stdout/stderr instead of to the console, nor the system RNG.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
* 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/MANOR.Rcheck/00check.log’
for details.


MANOR.Rcheck/00install.out:

* installing *source* package ‘MANOR’ ...
** libs
gcc -I/home/biocbuild/bbs-3.6-bioc/R/include -DNDEBUG   -I/usr/local/include   -fpic  -g -O2  -Wall -c Rnem_arg.c -o Rnem_arg.o
gcc -I/home/biocbuild/bbs-3.6-bioc/R/include -DNDEBUG   -I/usr/local/include   -fpic  -g -O2  -Wall -c Rnem_exe.c -o Rnem_exe.o
gcc -I/home/biocbuild/bbs-3.6-bioc/R/include -DNDEBUG   -I/usr/local/include   -fpic  -g -O2  -Wall -c exememo.c -o exememo.o
In file included from /home/biocbuild/bbs-3.6-bioc/R/include/R.h:86:0,
                 from exememo.c:20:
exememo.c: In function ‘GenAlloc’:
/home/biocbuild/bbs-3.6-bioc/R/include/R_ext/Error.h:52:15: warning: ‘msg’ may be used uninitialized in this function [-Wmaybe-uninitialized]
 #define error Rf_error
               ^
exememo.c:39:11: note: ‘msg’ was declared here
     char* msg;
           ^
gcc -I/home/biocbuild/bbs-3.6-bioc/R/include -DNDEBUG   -I/usr/local/include   -fpic  -g -O2  -Wall -c nem_alg.c -o nem_alg.o
gcc -I/home/biocbuild/bbs-3.6-bioc/R/include -DNDEBUG   -I/usr/local/include   -fpic  -g -O2  -Wall -c nem_hlp.c -o nem_hlp.o
gcc -I/home/biocbuild/bbs-3.6-bioc/R/include -DNDEBUG   -I/usr/local/include   -fpic  -g -O2  -Wall -c nem_mod.c -o nem_mod.o
gcc -I/home/biocbuild/bbs-3.6-bioc/R/include -DNDEBUG   -I/usr/local/include   -fpic  -g -O2  -Wall -c nem_nei.c -o nem_nei.o
gcc -I/home/biocbuild/bbs-3.6-bioc/R/include -DNDEBUG   -I/usr/local/include   -fpic  -g -O2  -Wall -c nem_rnd.c -o nem_rnd.o
gcc -I/home/biocbuild/bbs-3.6-bioc/R/include -DNDEBUG   -I/usr/local/include   -fpic  -g -O2  -Wall -c nem_ver.c -o nem_ver.o
gcc -shared -L/home/biocbuild/bbs-3.6-bioc/R/lib -L/usr/local/lib -o MANOR.so Rnem_arg.o Rnem_exe.o exememo.o nem_alg.o nem_hlp.o nem_mod.o nem_nei.o nem_rnd.o nem_ver.o -L/home/biocbuild/bbs-3.6-bioc/R/lib -lR
installing to /home/biocbuild/bbs-3.6-bioc/meat/MANOR.Rcheck/MANOR/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 (MANOR)

MANOR.Rcheck/MANOR-Ex.timings:

nameusersystemelapsed
arrayTrend0.4280.0040.431
detectSB0.4480.0080.456
flag.arrayCGH1.0360.0001.037
flag.summary0.0960.0000.096
flags0.1000.0040.105
genome.plot0.3680.0000.365
import0.2320.0000.232
nem4.120.004.12
norm0.7000.0080.709
qscore.arrayCGH0.0920.0000.090
qscore.summary0.4160.0040.418
qscores0.4240.0120.439
report.plot0.8040.0040.810
sort0.1720.0040.175
spatial0.2720.0040.274
to.flag0.3880.0040.395