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This page was generated on 2021-10-22 12:03:54 -0400 (Fri, 22 Oct 2021).

CHECK results for ACME on nebbiolo2

To the developers/maintainers of the ACME package:
- Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/ACME.git to
reflect on this report. See How and When does the builder pull? When will my changes propagate? here for more information.
- Make sure to use the following settings in order to reproduce any error or warning you see on this page.

raw results

Package 14/2075HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
ACME 2.49.0  (landing page)
Sean Davis
Snapshot Date: 2021-10-21 14:50:08 -0400 (Thu, 21 Oct 2021)
git_url: https://git.bioconductor.org/packages/ACME
git_branch: master
git_last_commit: adb1ab3
git_last_commit_date: 2021-05-19 11:38:59 -0400 (Wed, 19 May 2021)
nebbiolo2Linux (Ubuntu 20.04.2 LTS) / x86_64  OK    OK    WARNINGS  UNNEEDED, same version is already published
riesling1Windows Server 2019 Standard / x64  OK    OK    WARNINGS    OK  UNNEEDED, same version is already published
merida1macOS 10.14.6 Mojave / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published

Summary

Package: ACME
Version: 2.49.0
Command: /home/biocbuild/bbs-3.14-bioc/R/bin/R CMD check --install=check:ACME.install-out.txt --library=/home/biocbuild/bbs-3.14-bioc/R/library --no-vignettes --timings ACME_2.49.0.tar.gz
StartedAt: 2021-10-21 19:04:13 -0400 (Thu, 21 Oct 2021)
EndedAt: 2021-10-21 19:05:10 -0400 (Thu, 21 Oct 2021)
EllapsedTime: 56.7 seconds
RetCode: 0
Status:   WARNINGS  
CheckDir: ACME.Rcheck
Warnings: 1

Command output

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### Running command:
###
###   /home/biocbuild/bbs-3.14-bioc/R/bin/R CMD check --install=check:ACME.install-out.txt --library=/home/biocbuild/bbs-3.14-bioc/R/library --no-vignettes --timings ACME_2.49.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.14-bioc/meat/ACME.Rcheck’
* using R version 4.1.1 (2021-08-10)
* 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 ‘2.49.0’
* 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 of ‘void * (*)()’ from incompatible pointer type ‘struct SEXPREC * (*)(struct SEXPREC *, struct SEXPREC *, struct SEXPREC *, struct SEXPREC *, struct SEXPREC *)’ [-Wincompatible-pointer-types]
See ‘/home/biocbuild/bbs-3.14-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 : <anonymous>: 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
Examples with CPU (user + system) or elapsed time > 5s
                 user system elapsed
findClosestGene 1.311  0.031  10.463
* 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-3.14-bioc/meat/ACME.Rcheck/00check.log’
for details.



Installation output

ACME.Rcheck/00install.out

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###
### Running command:
###
###   /home/biocbuild/bbs-3.14-bioc/R/bin/R CMD INSTALL ACME
###
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* installing to library ‘/home/biocbuild/bbs-3.14-bioc/R/library’
* installing *source* package ‘ACME’ ...
** using staged installation
** libs
gcc -I"/home/biocbuild/bbs-3.14-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]
   58 |    firstprobe>0) {
      |    ~~~~~~~~~~^~
windowChisq.c:63:13: warning: suggest parentheses around comparison in operand of ‘&’ [-Wparentheses]
   63 |    lastprobe<(na-1)) {
      |    ~~~~~~~~~^~~~~~~
windowChisq.c:21:11: warning: unused variable ‘xa’ [-Wunused-variable]
   21 |   double *xa,*xlocations,*xchivals;
      |           ^~
windowChisq.c: At top level:
windowChisq.c:86:20: warning: initialization of ‘void * (*)()’ from incompatible pointer type ‘struct SEXPREC * (*)(struct SEXPREC *, struct SEXPREC *, struct SEXPREC *, struct SEXPREC *, struct SEXPREC *)’ [-Wincompatible-pointer-types]
   86 |     {"windowChisq",&windowChisq,5},
      |                    ^
windowChisq.c:86:20: note: (near initialization for ‘callMethods[0].fun’)
gcc -shared -L/home/biocbuild/bbs-3.14-bioc/R/lib -L/usr/local/lib -o ACME.so windowChisq.o -L/home/biocbuild/bbs-3.14-bioc/R/lib -lR
installing to /home/biocbuild/bbs-3.14-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)

Tests output


Example timings

ACME.Rcheck/ACME-Ex.timings

nameusersystemelapsed
ACMECalcSet-class1.2130.0491.261
ACMESet-class0.4720.0120.484
aGFF-class0.4770.0160.493
aGFFCalc-class1.1390.0281.167
do.aGFF.calc1.1520.0081.160
example.agff0.4400.0120.452
findClosestGene 1.311 0.03110.463
findRegions2.540.022.56
generics0.6270.0030.631
getRefflat1.3190.0122.355
read.resultsGFF3.4970.0483.545
write.bedGraph1.5730.0201.593
write.sgr1.4590.0201.480