Sean Davis
| Snapshot Date: 2019-10-15 17:01:26 -0400 (Tue, 15 Oct 2019) |
| URL: https://git.bioconductor.org/packages/ACME |
| Branch: RELEASE_3_9 |
| Last Commit: 38499e5 |
| Last Changed Date: 2019-05-02 11:53:07 -0400 (Thu, 02 May 2019) |
| Back to Multiple platform build/check report for BioC 3.9 |
|
This page was generated on 2019-10-16 11:56:30 -0400 (Wed, 16 Oct 2019).
| Package 14/1741 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
| ACME 2.40.0 Sean Davis
| malbec2 | Linux (Ubuntu 18.04.2 LTS) / x86_64 | OK | OK | [ WARNINGS ] | | ||||||
| tokay2 | Windows Server 2012 R2 Standard / x64 | OK | OK | WARNINGS | OK | | ||||||
| celaya2 | OS X 10.11.6 El Capitan / x86_64 | OK | OK | OK | OK | |
| Package: ACME |
| Version: 2.40.0 |
| Command: /home/biocbuild/bbs-3.9-bioc/R/bin/R CMD check --install=check:ACME.install-out.txt --library=/home/biocbuild/bbs-3.9-bioc/R/library --no-vignettes --timings ACME_2.40.0.tar.gz |
| StartedAt: 2019-10-15 23:37:33 -0400 (Tue, 15 Oct 2019) |
| EndedAt: 2019-10-15 23:38:36 -0400 (Tue, 15 Oct 2019) |
| EllapsedTime: 63.5 seconds |
| RetCode: 0 |
| Status: WARNINGS |
| CheckDir: ACME.Rcheck |
| Warnings: 1 |
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### Running command:
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### /home/biocbuild/bbs-3.9-bioc/R/bin/R CMD check --install=check:ACME.install-out.txt --library=/home/biocbuild/bbs-3.9-bioc/R/library --no-vignettes --timings ACME_2.40.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.9-bioc/meat/ACME.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 ‘ACME/DESCRIPTION’ ... OK
* this is package ‘ACME’ version ‘2.40.0’
* 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 ‘ACME’ can be installed ... WARNING
Found the following significant warnings:
windowChisq.c:58:14: warning: suggest parentheses around comparison in operand of ‘&’ [-Wparentheses]
windowChisq.c:63:13: warning: suggest parentheses around comparison in operand of ‘&’ [-Wparentheses]
windowChisq.c:86:20: warning: initialization from incompatible pointer type [-Wincompatible-pointer-types]
See ‘/home/biocbuild/bbs-3.9-bioc/meat/ACME.Rcheck/00install.out’ for details.
* checking installed package size ... NOTE
installed size is 30.8Mb
sub-directories of 1Mb or more:
data 3.1Mb
extdata 27.3Mb
* 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 ... NOTE
.plotACMECalcSet: no visible global function definition for ‘par’
.plotACMECalcSet: no visible global function definition for ‘axis’
.plotACMECalcSet: no visible global function definition for ‘abline’
.plotACMESet: no visible global function definition for ‘par’
do.aGFF.calc: no visible global function definition for ‘quantile’
findClosestGene: no visible binding for global variable ‘refflat’
findClosestGene: no visible binding for '<<-' assignment to ‘refflat’
findRegions : : no visible global function definition for
‘median’
getRefflat: no visible global function definition for ‘download.file’
getRefflat: no visible global function definition for ‘read.delim’
plotgff: no visible global function definition for ‘par’
plotgffcalc: no visible global function definition for ‘par’
plotgffcalc: no visible global function definition for ‘axis’
plotgffcalc: no visible global function definition for ‘abline’
read.resultsGFF: no visible global function definition for ‘read.delim’
windowChisq: no visible global function definition for ‘pchisq’
write.bedGraph: no visible global function definition for ‘write.table’
write.sgr: no visible global function definition for ‘write.table’
plot,ACMECalcSet: no visible global function definition for ‘par’
plot,ACMECalcSet: no visible global function definition for ‘axis’
plot,ACMECalcSet: no visible global function definition for ‘abline’
plot,ACMESet: no visible global function definition for ‘par’
plot,aGFF: no visible global function definition for ‘par’
plot,aGFFCalc: no visible global function definition for ‘par’
plot,aGFFCalc: no visible global function definition for ‘axis’
plot,aGFFCalc: no visible global function definition for ‘abline’
Undefined global functions or variables:
abline axis download.file median par pchisq quantile read.delim
refflat write.table
Consider adding
importFrom("graphics", "abline", "axis", "par")
importFrom("stats", "median", "pchisq", "quantile")
importFrom("utils", "download.file", "read.delim", "write.table")
to your NAMESPACE file.
* 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 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: 1 WARNING, 3 NOTEs
See
‘/home/biocbuild/bbs-3.9-bioc/meat/ACME.Rcheck/00check.log’
for details.
ACME.Rcheck/00install.out
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### Running command:
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### /home/biocbuild/bbs-3.9-bioc/R/bin/R CMD INSTALL ACME
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* installing to library ‘/home/biocbuild/bbs-3.9-bioc/R/library’
* installing *source* package ‘ACME’ ...
** using staged installation
** libs
gcc -I"/home/biocbuild/bbs-3.9-bioc/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -Wall -c windowChisq.c -o windowChisq.o
windowChisq.c: In function ‘windowChisq’:
windowChisq.c:58:14: warning: suggest parentheses around comparison in operand of ‘&’ [-Wparentheses]
firstprobe>0) {
~~~~~~~~~~^~
windowChisq.c:63:13: warning: suggest parentheses around comparison in operand of ‘&’ [-Wparentheses]
lastprobe<(na-1)) {
~~~~~~~~~^~~~~~~
windowChisq.c:21:11: warning: unused variable ‘xa’ [-Wunused-variable]
double *xa,*xlocations,*xchivals;
^~
windowChisq.c: At top level:
windowChisq.c:86:20: warning: initialization from incompatible pointer type [-Wincompatible-pointer-types]
{"windowChisq",&windowChisq,5},
^
windowChisq.c:86:20: note: (near initialization for ‘callMethods[0].fun’)
gcc -shared -L/home/biocbuild/bbs-3.9-bioc/R/lib -L/usr/local/lib -o ACME.so windowChisq.o -L/home/biocbuild/bbs-3.9-bioc/R/lib -lR
installing to /home/biocbuild/bbs-3.9-bioc/R/library/00LOCK-ACME/00new/ACME/libs
** R
** data
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** 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 (ACME)
ACME.Rcheck/ACME-Ex.timings
| name | user | system | elapsed | |
| ACMECalcSet-class | 1.564 | 0.028 | 1.592 | |
| ACMESet-class | 0.555 | 0.012 | 0.566 | |
| aGFF-class | 0.457 | 0.008 | 0.465 | |
| aGFFCalc-class | 1.314 | 0.016 | 1.330 | |
| do.aGFF.calc | 1.176 | 0.008 | 1.185 | |
| example.agff | 0.591 | 0.008 | 0.599 | |
| findClosestGene | 2.264 | 0.037 | 4.276 | |
| findRegions | 3.558 | 0.032 | 3.598 | |
| generics | 0.658 | 0.012 | 0.670 | |
| getRefflat | 2.627 | 0.016 | 4.859 | |
| read.resultsGFF | 3.552 | 0.048 | 3.963 | |
| write.bedGraph | 2.355 | 0.040 | 2.395 | |
| write.sgr | 2.487 | 0.028 | 2.517 | |