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CHECK report for ACME on tokay1

This page was generated on 2020-08-09 11:57:26 -0400 (Sun, 09 Aug 2020).

TO THE DEVELOPERS/MAINTAINERS OF THE ACME PACKAGE: Please make sure to use the following settings in order to reproduce any error or warning you see on this page.
Package 14/1882HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
ACME 2.45.0
Sean Davis
Snapshot Date: 2020-08-08 14:51:01 -0400 (Sat, 08 Aug 2020)
URL: https://git.bioconductor.org/packages/ACME
Branch: master
Last Commit: 58f42e2
Last Changed Date: 2020-04-27 14:15:01 -0400 (Mon, 27 Apr 2020)
malbec1 Linux (Ubuntu 18.04.4 LTS) / x86_64  OK  OK  WARNINGS UNNEEDED, same version exists in internal repository
nebbiolo1 Linux (Ubuntu 20.04.1 LTS) / x86_64  OK  OK  WARNINGS 
tokay1 Windows Server 2012 R2 Standard / x64  OK  OK [ WARNINGS ] 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: ACME
Version: 2.45.0
Command: C:\Users\biocbuild\bbs-3.12-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:ACME.install-out.txt --library=C:\Users\biocbuild\bbs-3.12-bioc\R\library --no-vignettes --timings ACME_2.45.0.tar.gz
StartedAt: 2020-08-08 23:48:12 -0400 (Sat, 08 Aug 2020)
EndedAt: 2020-08-08 23:50:17 -0400 (Sat, 08 Aug 2020)
EllapsedTime: 125.4 seconds
RetCode: 0
Status:  WARNINGS  
CheckDir: ACME.Rcheck
Warnings: 1

Command output

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###
### Running command:
###
###   C:\Users\biocbuild\bbs-3.12-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:ACME.install-out.txt --library=C:\Users\biocbuild\bbs-3.12-bioc\R\library --no-vignettes --timings ACME_2.45.0.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.12-bioc/meat/ACME.Rcheck'
* using R version 4.0.2 (2020-06-22)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'ACME/DESCRIPTION' ... OK
* this is package 'ACME' version '2.45.0'
* 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 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 'C:/Users/biocbuild/bbs-3.12-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
* loading checks for arch 'i386'
** 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
* loading checks for arch 'x64'
** 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 for i386 is not available
Note: information on .o files for x64 is not available
File 'C:/Users/biocbuild/bbs-3.12-bioc/R/library/ACME/libs/i386/ACME.dll':
  Found 'abort', possibly from 'abort' (C), 'runtime' (Fortran)
File 'C:/Users/biocbuild/bbs-3.12-bioc/R/library/ACME/libs/x64/ACME.dll':
  Found 'abort', possibly from 'abort' (C), 'runtime' (Fortran)

Compiled code should not call entry points which might terminate R nor
write to stdout/stderr instead of to the console, nor use Fortran I/O
nor system RNGs. The detected symbols are linked into the code but
might come from libraries and not actually be called.

See 'Writing portable packages' in the 'Writing R Extensions' manual.
* checking files in 'vignettes' ... OK
* checking examples ...
** running examples for arch 'i386' ... OK
Examples with CPU (user + system) or elapsed time > 5s
                user system elapsed
write.bedGraph  5.15   0.08    9.61
read.resultsGFF 4.00   0.09    7.40
** running examples for arch 'x64' ... 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
  'C:/Users/biocbuild/bbs-3.12-bioc/meat/ACME.Rcheck/00check.log'
for details.



Installation output

ACME.Rcheck/00install.out

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###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O https://malbec1.bioconductor.org/BBS/3.12/bioc/src/contrib/ACME_2.45.0.tar.gz && rm -rf ACME.buildbin-libdir && mkdir ACME.buildbin-libdir && C:\Users\biocbuild\bbs-3.12-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=ACME.buildbin-libdir ACME_2.45.0.tar.gz && C:\Users\biocbuild\bbs-3.12-bioc\R\bin\R.exe CMD INSTALL ACME_2.45.0.zip && rm ACME_2.45.0.tar.gz ACME_2.45.0.zip
###
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  % Total    % Received % Xferd  Average Speed   Time    Time     Time  Current
                                 Dload  Upload   Total   Spent    Left  Speed

  0     0    0     0    0     0      0      0 --:--:-- --:--:-- --:--:--     0
100 9441k  100 9441k    0     0  76.7M      0 --:--:-- --:--:-- --:--:-- 79.4M

install for i386

* installing *source* package 'ACME' ...
** using staged installation
** libs
"C:/rtools40/mingw32/bin/"gcc  -I"C:/Users/BIOCBU~1/BBS-3~1.12-/R/include" -DNDEBUG     -I"C:/extsoft/include"     -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -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 of 'void * (*)()' from incompatible pointer type 'struct SEXPREC * (*)(struct SEXPREC *, struct SEXPREC *, struct SEXPREC *, struct SEXPREC *, struct SEXPREC *)' [-Wincompatible-pointer-types]
     {"windowChisq",&windowChisq,5},
                    ^
windowChisq.c:86:20: note: (near initialization for 'callMethods[0].fun')
C:/rtools40/mingw32/bin/gcc -shared -s -static-libgcc -o ACME.dll tmp.def windowChisq.o -LC:/extsoft/lib/i386 -LC:/extsoft/lib -LC:/Users/BIOCBU~1/BBS-3~1.12-/R/bin/i386 -lR
installing to C:/Users/biocbuild/bbs-3.12-bioc/meat/ACME.buildbin-libdir/00LOCK-ACME/00new/ACME/libs/i386
** R
** data
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
  converting help for package 'ACME'
    finding HTML links ... done
    ACMECalcSet-class                       html  
    finding level-2 HTML links ... done

    ACMESet-class                           html  
    aGFF-class                              html  
    aGFFCalc-class                          html  
    do.aGFF.calc                            html  
    example.agff                            html  
    findClosestGene                         html  
    findRegions                             html  
    generics                                html  
    getRefflat                              html  
    read.resultsGFF                         html  
    write.bedGraph                          html  
    write.sgr                               html  
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path

install for x64

* installing *source* package 'ACME' ...
** libs
"C:/rtools40/mingw64/bin/"gcc  -I"C:/Users/BIOCBU~1/BBS-3~1.12-/R/include" -DNDEBUG     -I"C:/extsoft/include"     -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -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 of 'void * (*)()' from incompatible pointer type 'struct SEXPREC * (*)(struct SEXPREC *, struct SEXPREC *, struct SEXPREC *, struct SEXPREC *, struct SEXPREC *)' [-Wincompatible-pointer-types]
     {"windowChisq",&windowChisq,5},
                    ^
windowChisq.c:86:20: note: (near initialization for 'callMethods[0].fun')
C:/rtools40/mingw64/bin/gcc -shared -s -static-libgcc -o ACME.dll tmp.def windowChisq.o -LC:/extsoft/lib/x64 -LC:/extsoft/lib -LC:/Users/BIOCBU~1/BBS-3~1.12-/R/bin/x64 -lR
installing to C:/Users/biocbuild/bbs-3.12-bioc/meat/ACME.buildbin-libdir/ACME/libs/x64
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'ACME' as ACME_2.45.0.zip
* DONE (ACME)
* installing to library 'C:/Users/biocbuild/bbs-3.12-bioc/R/library'
package 'ACME' successfully unpacked and MD5 sums checked

Tests output


Example timings

ACME.Rcheck/examples_i386/ACME-Ex.timings

nameusersystemelapsed
ACMECalcSet-class2.000.142.14
ACMESet-class0.850.020.86
aGFF-class0.850.030.87
aGFFCalc-class2.310.092.41
do.aGFF.calc1.840.061.90
example.agff0.670.030.71
findClosestGene1.720.044.87
findRegions3.560.063.62
generics0.580.030.61
getRefflat1.270.103.46
read.resultsGFF4.000.097.40
write.bedGraph5.150.089.61
write.sgr3.440.113.55

ACME.Rcheck/examples_x64/ACME-Ex.timings

nameusersystemelapsed
ACMECalcSet-class1.390.081.47
ACMESet-class0.440.030.47
aGFF-class0.420.030.45
aGFFCalc-class1.330.101.42
do.aGFF.calc1.250.061.32
example.agff0.430.030.46
findClosestGene1.570.083.13
findRegions2.840.112.95
generics0.440.010.46
getRefflat1.570.113.00
read.resultsGFF3.160.043.18
write.bedGraph3.810.144.11
write.sgr2.740.042.78