Ramon Diaz-Uriarte
| Snapshot Date: 2019-10-15 17:01:26 -0400 (Tue, 15 Oct 2019) |
| URL: https://git.bioconductor.org/packages/ADaCGH2 |
| Branch: RELEASE_3_9 |
| Last Commit: 875a4c9 |
| Last Changed Date: 2019-05-02 11:53:19 -0400 (Thu, 02 May 2019) |
| Back to Multiple platform build/check report for BioC 3.9 |
|
This page was generated on 2019-10-16 11:59:05 -0400 (Wed, 16 Oct 2019).
| Package 15/1741 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
| ADaCGH2 2.24.0 Ramon Diaz-Uriarte
| malbec2 | Linux (Ubuntu 18.04.2 LTS) / x86_64 | OK | OK | [ OK ] | | ||||||
| tokay2 | Windows Server 2012 R2 Standard / x64 | OK | OK | OK | OK | | ||||||
| celaya2 | OS X 10.11.6 El Capitan / x86_64 | OK | OK | OK | OK | |
| Package: ADaCGH2 |
| Version: 2.24.0 |
| Command: /home/biocbuild/bbs-3.9-bioc/R/bin/R CMD check --install=check:ADaCGH2.install-out.txt --library=/home/biocbuild/bbs-3.9-bioc/R/library --no-vignettes --timings ADaCGH2_2.24.0.tar.gz |
| StartedAt: 2019-10-15 23:37:33 -0400 (Tue, 15 Oct 2019) |
| EndedAt: 2019-10-15 23:40:33 -0400 (Tue, 15 Oct 2019) |
| EllapsedTime: 180.3 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: ADaCGH2.Rcheck |
| Warnings: 0 |
##############################################################################
##############################################################################
###
### Running command:
###
### /home/biocbuild/bbs-3.9-bioc/R/bin/R CMD check --install=check:ADaCGH2.install-out.txt --library=/home/biocbuild/bbs-3.9-bioc/R/library --no-vignettes --timings ADaCGH2_2.24.0.tar.gz
###
##############################################################################
##############################################################################
* using log directory ‘/home/biocbuild/bbs-3.9-bioc/meat/ADaCGH2.Rcheck’
* using R version 3.6.1 (2019-07-05)
* 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 ‘2.24.0’
* 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 37.018 6.776 21.388
pChromPlot 29.198 11.763 5.779
outputToCGHregions 25.108 4.260 8.595
inputToADaCGH 5.271 1.061 5.994
* 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-3.9-bioc/meat/ADaCGH2.Rcheck/00check.log’
for details.
ADaCGH2.Rcheck/00install.out
##############################################################################
##############################################################################
###
### Running command:
###
### /home/biocbuild/bbs-3.9-bioc/R/bin/R CMD INSTALL ADaCGH2
###
##############################################################################
##############################################################################
* installing to library ‘/home/biocbuild/bbs-3.9-bioc/R/library’
* installing *source* package ‘ADaCGH2’ ...
** using staged installation
** libs
gcc -I"/home/biocbuild/bbs-3.9-bioc/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -Wall -c init.c -o init.o
gcc -I"/home/biocbuild/bbs-3.9-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-3.9-bioc/R/lib -L/usr/local/lib -o ADaCGH2.so init.o r_haarseg.o -L/home/biocbuild/bbs-3.9-bioc/R/lib -lR
installing to /home/biocbuild/bbs-3.9-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)
ADaCGH2.Rcheck/ADaCGH2-Ex.timings
| name | user | system | elapsed | |
| cutFile | 0.027 | 0.721 | 2.807 | |
| inputToADaCGH | 5.271 | 1.061 | 5.994 | |
| outputToCGHregions | 25.108 | 4.260 | 8.595 | |
| pChromPlot | 29.198 | 11.763 | 5.779 | |
| pSegment | 37.018 | 6.776 | 21.388 | |