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) |
| Back to Multiple platform build/check report for BioC 3.8 |
|
This page was generated on 2019-04-16 11:49:01 -0400 (Tue, 16 Apr 2019).
| Package 15/1649 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
| ADaCGH2 2.22.0 Ramon Diaz-Uriarte
| malbec1 | Linux (Ubuntu 16.04.6 LTS) / x86_64 | OK | OK | [ OK ] | | ||||||
| merida1 | OS X 10.11.6 El Capitan / x86_64 | OK | OK | OK | OK | |
| 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 |
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### Running command:
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### /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.
ADaCGH2.Rcheck/00install.out
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### Running command:
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### /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)
ADaCGH2.Rcheck/ADaCGH2-Ex.timings
| name | user | system | elapsed | |
| cutFile | 0.008 | 0.588 | 2.894 | |
| inputToADaCGH | 4.960 | 0.860 | 5.534 | |
| outputToCGHregions | 25.312 | 4.136 | 8.662 | |
| pChromPlot | 29.000 | 12.056 | 5.279 | |
| pSegment | 36.120 | 6.352 | 20.576 | |