Back to Multiple platform build/check report for BioC 3.13
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This page was generated on 2021-09-17 15:06:04 -0400 (Fri, 17 Sep 2021).

CHECK results for erma on tokay2

To the developers/maintainers of the erma package:
- Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/erma.git to
reflect on this report. See How and When does the builder pull? When will my changes propagate? here for more information.
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raw results

Package 593/2041HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
erma 1.8.0  (landing page)
VJ Carey
Snapshot Date: 2021-09-16 04:50:11 -0400 (Thu, 16 Sep 2021)
git_url: https://git.bioconductor.org/packages/erma
git_branch: RELEASE_3_13
git_last_commit: 6958ee9
git_last_commit_date: 2021-05-19 12:14:10 -0400 (Wed, 19 May 2021)
nebbiolo1Linux (Ubuntu 20.04.2 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
tokay2Windows Server 2012 R2 Standard / x64  OK    OK    OK    OK  UNNEEDED, same version is already published
machv2macOS 10.14.6 Mojave / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published

Summary

Package: erma
Version: 1.8.0
Command: C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:erma.install-out.txt --library=C:\Users\biocbuild\bbs-3.13-bioc\R\library --no-vignettes --timings erma_1.8.0.tar.gz
StartedAt: 2021-09-16 22:56:49 -0400 (Thu, 16 Sep 2021)
EndedAt: 2021-09-16 23:05:43 -0400 (Thu, 16 Sep 2021)
EllapsedTime: 534.1 seconds
RetCode: 0
Status:   OK  
CheckDir: erma.Rcheck
Warnings: 0

Command output

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###
### Running command:
###
###   C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:erma.install-out.txt --library=C:\Users\biocbuild\bbs-3.13-bioc\R\library --no-vignettes --timings erma_1.8.0.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.13-bioc/meat/erma.Rcheck'
* using R version 4.1.1 (2021-08-10)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'erma/DESCRIPTION' ... OK
* this is package 'erma' version '1.8.0'
* 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 'erma' can be installed ... OK
* checking installed package size ... NOTE
  installed size is 199.3Mb
  sub-directories of 1Mb or more:
    bed_tabix  161.4Mb
    data        37.1Mb
* 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
geneTxRange: no visible global function definition for 'select'
genemodelOLD: no visible binding for global variable 'exonsBy'
stateProfile: no visible binding for global variable 'states_25'
stateProfile: no visible binding for global variable 'short_celltype'
stateProfile: no visible binding for global variable 'name'
statesByRange: no visible binding for global variable 'mod'
statesByRange: no visible binding for global variable 'upstream'
statesByRange: no visible binding for global variable 'downstream'
statesByRange : <anonymous>: no visible binding for global variable
  'tss'
statesByRange: no visible binding for global variable 'states_25'
Undefined global functions or variables:
  downstream exonsBy mod name select short_celltype states_25 tss
  upstream
* 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 files in 'vignettes' ... OK
* checking examples ...
** running examples for arch 'i386' ... OK
Examples with CPU (user + system) or elapsed time > 5s
             user system elapsed
erma-package 10.5   0.44   27.72
stateProfile  3.4   0.03   20.60
** running examples for arch 'x64' ... OK
Examples with CPU (user + system) or elapsed time > 5s
             user system elapsed
erma-package 9.14   0.37   27.67
stateProfile 3.79   0.08   23.64
* 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: 2 NOTEs
See
  'C:/Users/biocbuild/bbs-3.13-bioc/meat/erma.Rcheck/00check.log'
for details.



Installation output

erma.Rcheck/00install.out

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###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O http://155.52.207.165/BBS/3.13/bioc/src/contrib/erma_1.8.0.tar.gz && rm -rf erma.buildbin-libdir && mkdir erma.buildbin-libdir && C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=erma.buildbin-libdir erma_1.8.0.tar.gz && C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD INSTALL erma_1.8.0.zip && rm erma_1.8.0.tar.gz erma_1.8.0.zip
###
##############################################################################
##############################################################################


  % Total    % Received % Xferd  Average Speed   Time    Time     Time  Current
                                 Dload  Upload   Total   Spent    Left  Speed

  0     0    0     0    0     0      0      0 --:--:-- --:--:-- --:--:--     0
  0  197M    0   99k    0     0   526k      0  0:06:24 --:--:--  0:06:24  526k
  1  197M    1 2977k    0     0  2522k      0  0:01:20  0:00:01  0:01:19 2521k
  3  197M    3 6691k    0     0  3061k      0  0:01:05  0:00:02  0:01:03 3061k
  5  197M    5 11.0M    0     0  3574k      0  0:00:56  0:00:03  0:00:53 3574k
  7  197M    7 14.8M    0     0  3618k      0  0:00:55  0:00:04  0:00:51 3618k
  9  197M    9 18.2M    0     0  3603k      0  0:00:56  0:00:05  0:00:51 3720k
 10  197M   10 20.4M    0     0  3294k      0  0:01:01  0:00:06  0:00:55 3471k
 11  197M   11 22.3M    0     0  3198k      0  0:01:03  0:00:07  0:00:56 3257k
 12  197M   12 24.2M    0     0  3041k      0  0:01:06  0:00:08  0:00:58 2704k
 12  197M   12 24.3M    0     0  2706k      0  0:01:14  0:00:09  0:01:05 1942k
 13  197M   13 26.8M    0     0  2705k      0  0:01:14  0:00:10  0:01:04 1765k
 15  197M   15 30.1M    0     0  2759k      0  0:01:13  0:00:11  0:01:02 2051k
 17  197M   17 34.4M    0     0  2899k      0  0:01:09  0:00:12  0:00:57 2470k
 18  197M   18 35.6M    0     0  2761k      0  0:01:13  0:00:13  0:01:00 2306k
 18  197M   18 35.6M    0     0  2569k      0  0:01:18  0:00:14  0:01:04 2317k
 18  197M   18 37.3M    0     0  2517k      0  0:01:20  0:00:15  0:01:05 2136k
 20  197M   20 40.3M    0     0  2550k      0  0:01:19  0:00:16  0:01:03 2084k
 22  197M   22 43.9M    0     0  2617k      0  0:01:17  0:00:17  0:01:00 1934k
 24  197M   24 48.3M    0     0  2724k      0  0:01:14  0:00:18  0:00:56 2625k
 27  197M   27 53.6M    0     0  2863k      0  0:01:10  0:00:19  0:00:51 3701k
 30  197M   30 59.4M    0     0  3019k      0  0:01:06  0:00:20  0:00:46 4553k
 33  197M   33 66.8M    0     0  3232k      0  0:01:02  0:00:21  0:00:41 5456k
 38  197M   38 75.0M    0     0  3466k      0  0:00:58  0:00:22  0:00:36 6396k
 42  197M   42 84.1M    0     0  3719k      0  0:00:54  0:00:23  0:00:31 7352k
 47  197M   47 93.7M    0     0  3969k      0  0:00:50  0:00:24  0:00:26 8217k
 53  197M   53  104M    0     0  4256k      0  0:00:47  0:00:25  0:00:22 9243k
 58  197M   58  116M    0     0  4550k      0  0:00:44  0:00:26  0:00:18  9.8M
 65  197M   65  128M    0     0  4851k      0  0:00:41  0:00:27  0:00:14 10.7M
 72  197M   72  142M    0     0  5172k      0  0:00:39  0:00:28  0:00:11 11.6M
 79  197M   79  156M    0     0  5504k      0  0:00:36  0:00:29  0:00:07 12.6M
 86  197M   86  171M    0     0  5811k      0  0:00:34  0:00:30  0:00:04 13.3M
 92  197M   92  183M    0     0  6017k      0  0:00:33  0:00:31  0:00:02 13.3M
100  197M  100  197M    0     0  6296k      0  0:00:32  0:00:32 --:--:-- 13.9M

install for i386

* installing *source* package 'erma' ...
** using staged installation
** R
** data
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
  converting help for package 'erma'
    finding HTML links ... done
    ErmaSet-class                           html  
    finding level-2 HTML links ... done

    erma-package                            html  
    genemodel                               html  
    mapmeta                                 html  
    stateProfile                            html  
    states_25                               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 'erma' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'erma' as erma_1.8.0.zip
* DONE (erma)
* installing to library 'C:/Users/biocbuild/bbs-3.13-bioc/R/library'
package 'erma' successfully unpacked and MD5 sums checked

Tests output


Example timings

erma.Rcheck/examples_i386/erma-Ex.timings

nameusersystemelapsed
ErmaSet-class0.360.200.58
erma-package10.50 0.4427.72
genemodel1.370.081.45
mapmeta0.210.000.20
stateProfile 3.40 0.0320.60
states_25000

erma.Rcheck/examples_x64/erma-Ex.timings

nameusersystemelapsed
ErmaSet-class0.410.020.42
erma-package 9.14 0.3727.67
genemodel1.400.071.48
mapmeta0.210.000.21
stateProfile 3.79 0.0823.64
states_250.020.000.01