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CHECK report for ACME on tokay1

This page was generated on 2020-04-15 12:18:01 -0400 (Wed, 15 Apr 2020).

Package 14/1823HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
ACME 2.42.0
Sean Davis
Snapshot Date: 2020-04-14 16:46:13 -0400 (Tue, 14 Apr 2020)
URL: https://git.bioconductor.org/packages/ACME
Branch: RELEASE_3_10
Last Commit: 7f41657
Last Changed Date: 2019-10-29 13:07:47 -0400 (Tue, 29 Oct 2019)
malbec1 Linux (Ubuntu 18.04.4 LTS) / x86_64  OK  OK  WARNINGS UNNEEDED, same version exists in internal repository
tokay1 Windows Server 2012 R2 Standard / x64  OK  OK [ WARNINGS ] OK UNNEEDED, same version exists in internal repository
merida1 OS X 10.11.6 El Capitan / x86_64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: ACME
Version: 2.42.0
Command: C:\Users\biocbuild\bbs-3.10-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:ACME.install-out.txt --library=C:\Users\biocbuild\bbs-3.10-bioc\R\library --no-vignettes --timings ACME_2.42.0.tar.gz
StartedAt: 2020-04-15 01:09:19 -0400 (Wed, 15 Apr 2020)
EndedAt: 2020-04-15 01:11:42 -0400 (Wed, 15 Apr 2020)
EllapsedTime: 143.0 seconds
RetCode: 0
Status:  WARNINGS  
CheckDir: ACME.Rcheck
Warnings: 1

Command output

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###
### Running command:
###
###   C:\Users\biocbuild\bbs-3.10-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:ACME.install-out.txt --library=C:\Users\biocbuild\bbs-3.10-bioc\R\library --no-vignettes --timings ACME_2.42.0.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.10-bioc/meat/ACME.Rcheck'
* using R version 3.6.3 (2020-02-29)
* 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 '2.42.0'
* 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]
See 'C:/Users/biocbuild/bbs-3.10-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-3.10-bioc/R/library/ACME/libs/i386/ACME.dll':
  Found 'abort', possibly from 'abort' (C), 'runtime' (Fortran)
File 'C:/Users/biocbuild/bbs-3.10-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 or elapsed time > 5s
                user system elapsed
read.resultsGFF 4.14   0.08    8.34
** 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-3.10-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/3.10/bioc/src/contrib/ACME_2.42.0.tar.gz && rm -rf ACME.buildbin-libdir && mkdir ACME.buildbin-libdir && C:\Users\biocbuild\bbs-3.10-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=ACME.buildbin-libdir ACME_2.42.0.tar.gz && C:\Users\biocbuild\bbs-3.10-bioc\R\bin\R.exe CMD INSTALL ACME_2.42.0.zip && rm ACME_2.42.0.tar.gz ACME_2.42.0.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
 60 9441k   60 5680k    0     0  39.6M      0 --:--:-- --:--:-- --:--:-- 40.1M
100 9441k  100 9441k    0     0  52.3M      0 --:--:-- --:--:-- --:--:-- 52.9M

install for i386

* installing *source* package 'ACME' ...
** using staged installation
** libs
C:/Rtools/mingw_32/bin/gcc  -I"C:/Users/BIOCBU~1/BBS-3~1.10-/R/include" -DNDEBUG     -I"C:/extsoft/include"     -O3 -Wall  -std=gnu99 -mtune=core2 -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:86:5: warning: initialization from incompatible pointer type
     {"windowChisq",&windowChisq,5},
     ^
windowChisq.c:86:5: warning: (near initialization for 'callMethods[0].fun')
C:/Rtools/mingw_32/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-3~1.10-/R/bin/i386 -lR
installing to C:/Users/biocbuild/bbs-3.10-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:/Rtools/mingw_64/bin/gcc  -I"C:/Users/BIOCBU~1/BBS-3~1.10-/R/include" -DNDEBUG     -I"C:/extsoft/include"     -O2 -Wall  -std=gnu99 -mtune=core2 -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:86:5: warning: initialization from incompatible pointer type
     {"windowChisq",&windowChisq,5},
     ^
windowChisq.c:86:5: warning: (near initialization for 'callMethods[0].fun')
C:/Rtools/mingw_64/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-3~1.10-/R/bin/x64 -lR
installing to C:/Users/biocbuild/bbs-3.10-bioc/meat/ACME.buildbin-libdir/ACME/libs/x64
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'ACME' as ACME_2.42.0.zip
* DONE (ACME)
* installing to library 'C:/Users/biocbuild/bbs-3.10-bioc/R/library'
package 'ACME' successfully unpacked and MD5 sums checked

Tests output


Example timings

ACME.Rcheck/examples_i386/ACME-Ex.timings

nameusersystemelapsed
ACMECalcSet-class2.010.112.13
ACMESet-class0.650.000.66
aGFF-class0.600.010.61
aGFFCalc-class1.670.071.73
do.aGFF.calc1.420.091.52
example.agff0.670.060.73
findClosestGene1.930.103.40
findRegions2.920.093.01
generics0.810.000.81
getRefflat2.770.114.43
read.resultsGFF4.140.088.34
write.bedGraph3.500.063.56
write.sgr2.660.092.75

ACME.Rcheck/examples_x64/ACME-Ex.timings

nameusersystemelapsed
ACMECalcSet-class1.770.001.77
ACMESet-class0.450.010.47
aGFF-class0.440.030.47
aGFFCalc-class1.340.041.37
do.aGFF.calc1.220.051.27
example.agff0.440.010.45
findClosestGene2.030.073.53
findRegions3.010.073.09
generics0.440.040.47
getRefflat2.110.064.52
read.resultsGFF2.890.092.98
write.bedGraph2.810.133.63
write.sgr2.280.042.33