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CHECK report for ADaCGH2 on nebbiolo1

This page was generated on 2020-11-27 11:54:25 -0500 (Fri, 27 Nov 2020).

TO THE DEVELOPERS/MAINTAINERS OF THE ADaCGH2 PACKAGE: Please make sure to use the following settings in order to reproduce any error or warning you see on this page.
Package 15/1974HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
ADaCGH2 2.30.0
Ramon Diaz-Uriarte
Snapshot Date: 2020-11-26 14:42:42 -0500 (Thu, 26 Nov 2020)
URL: https://git.bioconductor.org/packages/ADaCGH2
Branch: RELEASE_3_12
Last Commit: 1d62234
Last Changed Date: 2020-10-27 10:39:31 -0500 (Tue, 27 Oct 2020)
malbec1 Linux (Ubuntu 18.04.4 LTS) / x86_64  OK  OK  OK UNNEEDED, same version exists in internal repository
nebbiolo1 Linux (Ubuntu 20.04.1 LTS) / x86_64  OK  OK [ OK ]
tokay1 Windows Server 2012 R2 Standard / x64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository
merida1 macOS 10.14.6 Mojave / x86_64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: ADaCGH2
Version: 2.30.0
Command: /home/biocbuild/bbs-3.12-bioc/R/bin/R CMD check --install=check:ADaCGH2.install-out.txt --library=/home/biocbuild/bbs-3.12-bioc/R/library --no-vignettes --timings ADaCGH2_2.30.0.tar.gz
StartedAt: 2020-11-26 19:54:06 -0500 (Thu, 26 Nov 2020)
EndedAt: 2020-11-26 19:57:29 -0500 (Thu, 26 Nov 2020)
EllapsedTime: 203.4 seconds
RetCode: 0
Status:  OK 
CheckDir: ADaCGH2.Rcheck
Warnings: 0

Command output

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###
### Running command:
###
###   /home/biocbuild/bbs-3.12-bioc/R/bin/R CMD check --install=check:ADaCGH2.install-out.txt --library=/home/biocbuild/bbs-3.12-bioc/R/library --no-vignettes --timings ADaCGH2_2.30.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.12-bioc/meat/ADaCGH2.Rcheck’
* using R version 4.0.3 (2020-10-10)
* 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 ‘2.30.0’
* 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 ‘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 (user + system) or elapsed time > 5s
                     user system elapsed
pSegment           34.037  3.373  29.352
pChromPlot         23.616 10.676  17.650
outputToCGHregions 23.167  1.499  14.324
inputToADaCGH       5.038  0.332   5.257
* 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-3.12-bioc/meat/ADaCGH2.Rcheck/00check.log’
for details.



Installation output

ADaCGH2.Rcheck/00install.out

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###
### Running command:
###
###   /home/biocbuild/bbs-3.12-bioc/R/bin/R CMD INSTALL ADaCGH2
###
##############################################################################
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* installing to library ‘/home/biocbuild/bbs-3.12-bioc/R/library’
* installing *source* package ‘ADaCGH2’ ...
** using staged installation
** libs
gcc -I"/home/biocbuild/bbs-3.12-bioc/R/include" -DNDEBUG   -I/usr/local/include   -fpic  -g -O2  -Wall -c init.c -o init.o
gcc -I"/home/biocbuild/bbs-3.12-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]
   65 |     double totalNorm;
      |            ^~~~~~~~~
r_haarseg.c: In function ‘ad_FindLocalPeaks’:
r_haarseg.c:152:8: warning: "/*" within comment [-Wcomment]
  152 |       }/* for j */
      |         
r_haarseg.c:176:8: warning: "/*" within comment [-Wcomment]
  176 |       }/* for j */
      |         
r_haarseg.c:128:9: warning: unused variable ‘j’ [-Wunused-variable]
  128 |   int k,j;
      |         ^
r_haarseg.c: In function ‘ad_HaarConv’:
r_haarseg.c:99:27: warning: ‘highWeightSum’ may be used uninitialized in this function [-Wmaybe-uninitialized]
   99 |             highWeightSum += weight[highEnd] - weight[k-1];
      |             ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
r_haarseg.c:97:27: warning: ‘highNonNormed’ may be used uninitialized in this function [-Wmaybe-uninitialized]
   97 |             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]
   96 |             lowNonNormed += signal[lowEnd]*weight[lowEnd] - signal[k-1]*weight[k-1];
      |             ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
r_haarseg.c:98:26: warning: ‘lowWeightSum’ may be used uninitialized in this function [-Wmaybe-uninitialized]
   98 |             lowWeightSum += weight[k-1] - weight[lowEnd];
      |             ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
gcc -shared -L/home/biocbuild/bbs-3.12-bioc/R/lib -L/usr/local/lib -o ADaCGH2.so init.o r_haarseg.o -L/home/biocbuild/bbs-3.12-bioc/R/lib -lR
installing to /home/biocbuild/bbs-3.12-bioc/R/library/00LOCK-ADaCGH2/00new/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 from temporary location
** checking absolute paths in shared objects and dynamic libraries
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (ADaCGH2)

Tests output


Example timings

ADaCGH2.Rcheck/ADaCGH2-Ex.timings

nameusersystemelapsed
cutFile0.0590.0382.128
inputToADaCGH5.0380.3325.257
outputToCGHregions23.167 1.49914.324
pChromPlot23.61610.67617.650
pSegment34.037 3.37329.352