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CHECK report for ADaCGH2 on malbec1

This page was generated on 2019-04-16 11:49:01 -0400 (Tue, 16 Apr 2019).

Package 15/1649HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
ADaCGH2 2.22.0
Ramon Diaz-Uriarte
Snapshot Date: 2019-04-15 17:01:12 -0400 (Mon, 15 Apr 2019)
URL: https://git.bioconductor.org/packages/ADaCGH2
Branch: RELEASE_3_8
Last Commit: dc1b45b
Last Changed Date: 2018-10-30 11:41:46 -0400 (Tue, 30 Oct 2018)
malbec1 Linux (Ubuntu 16.04.6 LTS) / x86_64  OK  OK [ OK ]UNNEEDED, same version exists in internal repository
merida1 OS X 10.11.6 El Capitan / x86_64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: ADaCGH2
Version: 2.22.0
Command: /home/biocbuild/bbs-3.8-bioc/R/bin/R CMD check --install=check:ADaCGH2.install-out.txt --library=/home/biocbuild/bbs-3.8-bioc/R/library --no-vignettes --timings ADaCGH2_2.22.0.tar.gz
StartedAt: 2019-04-15 22:05:33 -0400 (Mon, 15 Apr 2019)
EndedAt: 2019-04-15 22:08:16 -0400 (Mon, 15 Apr 2019)
EllapsedTime: 163.3 seconds
RetCode: 0
Status:  OK 
CheckDir: ADaCGH2.Rcheck
Warnings: 0

Command output

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### Running command:
###
###   /home/biocbuild/bbs-3.8-bioc/R/bin/R CMD check --install=check:ADaCGH2.install-out.txt --library=/home/biocbuild/bbs-3.8-bioc/R/library --no-vignettes --timings ADaCGH2_2.22.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.8-bioc/meat/ADaCGH2.Rcheck’
* using R version 3.5.3 (2019-03-11)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘ADaCGH2/DESCRIPTION’ ... OK
* this is package ‘ADaCGH2’ version ‘2.22.0’
* 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 ‘ADaCGH2’ 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 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
Note: information on .o files is not available
* 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
pSegment           36.120  6.352  20.576
pChromPlot         29.000 12.056   5.279
outputToCGHregions 25.312  4.136   8.662
inputToADaCGH       4.960  0.860   5.534
* 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 NOTE
See
  ‘/home/biocbuild/bbs-3.8-bioc/meat/ADaCGH2.Rcheck/00check.log’
for details.



Installation output

ADaCGH2.Rcheck/00install.out

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###
### Running command:
###
###   /home/biocbuild/bbs-3.8-bioc/R/bin/R CMD INSTALL ADaCGH2
###
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* installing to library ‘/home/biocbuild/bbs-3.8-bioc/R/library’
* installing *source* package ‘ADaCGH2’ ...
** libs
gcc -I"/home/biocbuild/bbs-3.8-bioc/R/include" -DNDEBUG   -I/usr/local/include   -fpic  -g -O2  -Wall -c init.c -o init.o
gcc -I"/home/biocbuild/bbs-3.8-bioc/R/include" -DNDEBUG   -I/usr/local/include   -fpic  -g -O2  -Wall -c r_haarseg.c -o r_haarseg.o
r_haarseg.c: In function ‘ad_HaarConv’:
r_haarseg.c:65:12: warning: unused variable ‘totalNorm’ [-Wunused-variable]
     double totalNorm;
            ^
r_haarseg.c: In function ‘ad_FindLocalPeaks’:
r_haarseg.c:152:8: warning: "/*" within comment [-Wcomment]
       }/* for j */
        ^
r_haarseg.c:176:8: warning: "/*" within comment [-Wcomment]
       }/* for j */
        ^
r_haarseg.c:128:9: warning: unused variable ‘j’ [-Wunused-variable]
   int k,j;
         ^
r_haarseg.c: In function ‘ad_HaarConv’:
r_haarseg.c:97:27: warning: ‘highNonNormed’ may be used uninitialized in this function [-Wmaybe-uninitialized]
             highNonNormed += signal[highEnd]*weight[highEnd] - signal[k-1]*weight[k-1]; 
                           ^
r_haarseg.c:96:26: warning: ‘lowNonNormed’ may be used uninitialized in this function [-Wmaybe-uninitialized]
             lowNonNormed += signal[lowEnd]*weight[lowEnd] - signal[k-1]*weight[k-1];
                          ^
r_haarseg.c:99:27: warning: ‘highWeightSum’ may be used uninitialized in this function [-Wmaybe-uninitialized]
             highWeightSum += weight[highEnd] - weight[k-1];
                           ^
r_haarseg.c:98:26: warning: ‘lowWeightSum’ may be used uninitialized in this function [-Wmaybe-uninitialized]
             lowWeightSum += weight[k-1] - weight[lowEnd];
                          ^
gcc -shared -L/home/biocbuild/bbs-3.8-bioc/R/lib -L/usr/local/lib -o ADaCGH2.so init.o r_haarseg.o -L/home/biocbuild/bbs-3.8-bioc/R/lib -lR
installing to /home/biocbuild/bbs-3.8-bioc/R/library/ADaCGH2/libs
** R
** data
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
   ‘ADaCGH2.Rnw’ using ‘latin1’ 
** testing if installed package can be loaded
* DONE (ADaCGH2)

Tests output


Example timings

ADaCGH2.Rcheck/ADaCGH2-Ex.timings

nameusersystemelapsed
cutFile0.0080.5882.894
inputToADaCGH4.9600.8605.534
outputToCGHregions25.312 4.136 8.662
pChromPlot29.00012.056 5.279
pSegment36.120 6.35220.576