Back to Multiple platform build/check report for BioC 3.14
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This page was generated on 2022-01-14 13:06:21 -0500 (Fri, 14 Jan 2022).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 20.04.4 LTS)x86_644.1.2 (2021-11-01) -- "Bird Hippie" 4327
tokay2Windows Server 2012 R2 Standardx644.1.2 (2021-11-01) -- "Bird Hippie" 4076
machv2macOS 10.14.6 Mojavex86_644.1.2 (2021-11-01) -- "Bird Hippie" 4137
Click on any hostname to see more info about the system (e.g. compilers)      (*) as reported by 'uname -p', except on Windows and Mac OS X

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.
- Make sure to use the following settings in order to reproduce any error or warning you see on this page.

raw results

Package 602/2083HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
erma 1.10.0  (landing page)
VJ Carey
Snapshot Date: 2022-01-13 01:55:04 -0500 (Thu, 13 Jan 2022)
git_url: https://git.bioconductor.org/packages/erma
git_branch: RELEASE_3_14
git_last_commit: 8ff4f3c
git_last_commit_date: 2021-10-26 12:21:07 -0500 (Tue, 26 Oct 2021)
nebbiolo2Linux (Ubuntu 20.04.4 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: 1.10.0
Command: C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:erma.install-out.txt --library=C:\Users\biocbuild\bbs-3.14-bioc\R\library --no-vignettes --timings erma_1.10.0.tar.gz
StartedAt: 2022-01-13 19:05:06 -0500 (Thu, 13 Jan 2022)
EndedAt: 2022-01-13 19:13:51 -0500 (Thu, 13 Jan 2022)
EllapsedTime: 525.2 seconds
RetCode: 0
Status:   OK  
CheckDir: erma.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:erma.install-out.txt --library=C:\Users\biocbuild\bbs-3.14-bioc\R\library --no-vignettes --timings erma_1.10.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'C:/Users/biocbuild/bbs-3.14-bioc/meat/erma.Rcheck'
* using R version 4.1.2 (2021-11-01)
* 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 '1.10.0'
* 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 9.24   0.66   28.53
stateProfile 3.63   0.10   21.64
** running examples for arch 'x64' ... OK
Examples with CPU (user + system) or elapsed time > 5s
             user system elapsed
erma-package 8.82   0.23   26.55
stateProfile 4.55   0.08   24.36
* 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-3.14-bioc/meat/erma.Rcheck/00check.log'
for details.



Installation output

erma.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O http://155.52.207.166/BBS/3.14/bioc/src/contrib/erma_1.10.0.tar.gz && rm -rf erma.buildbin-libdir && mkdir erma.buildbin-libdir && C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=erma.buildbin-libdir erma_1.10.0.tar.gz && C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD INSTALL erma_1.10.0.zip && rm erma_1.10.0.tar.gz erma_1.10.0.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 1001k    0     0  2607k      0  0:01:17 --:--:--  0:01:17 2609k
  2  197M    2 5959k    0     0  4357k      0  0:00:46  0:00:01  0:00:45 4359k
  6  197M    6 12.3M    0     0  5348k      0  0:00:37  0:00:02  0:00:35 5348k
 10  197M   10 20.6M    0     0  6294k      0  0:00:32  0:00:03  0:00:29 6293k
 15  197M   15 30.1M    0     0  7066k      0  0:00:28  0:00:04  0:00:24 7066k
 18  197M   18 36.3M    0     0  6929k      0  0:00:29  0:00:05  0:00:24 7261k
 22  197M   22 44.5M    0     0  7165k      0  0:00:28  0:00:06  0:00:22 7934k
 27  197M   27 54.2M    0     0  7534k      0  0:00:26  0:00:07  0:00:19 8568k
 33  197M   33 65.6M    0     0  8033k      0  0:00:25  0:00:08  0:00:17 9206k
 39  197M   39 78.8M    0     0  8614k      0  0:00:23  0:00:09  0:00:14 9966k
 47  197M   47 92.8M    0     0  9168k      0  0:00:22  0:00:10  0:00:12 11.3M
 54  197M   54  106M    0     0  9617k      0  0:00:21  0:00:11  0:00:10 12.4M
 63  197M   63  124M    0     0  10.0M      0  0:00:19  0:00:12  0:00:07 14.0M
 72  197M   72  143M    0     0  10.7M      0  0:00:18  0:00:13  0:00:05 15.5M
 78  197M   78  153M    0     0  10.7M      0  0:00:18  0:00:14  0:00:04 15.0M
 80  197M   80  159M    0     0  10.3M      0  0:00:19  0:00:15  0:00:04 13.2M
 83  197M   83  165M    0     0  10.0M      0  0:00:19  0:00:16  0:00:03 11.6M
 87  197M   87  172M    0     0   9.9M      0  0:00:19  0:00:17  0:00:02 9893k
 92  197M   92  182M    0     0   9.9M      0  0:00:19  0:00:18  0:00:01 7975k
 98  197M   98  193M    0     0   9.9M      0  0:00:19  0:00:19 --:--:-- 8101k
100  197M  100  197M    0     0  10.0M      0  0:00:19  0:00:19 --:--:-- 9085k

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_1.10.0.zip
* DONE (erma)
* installing to library 'C:/Users/biocbuild/bbs-3.14-bioc/R/library'
package 'erma' successfully unpacked and MD5 sums checked

Tests output


Example timings

erma.Rcheck/examples_i386/erma-Ex.timings

nameusersystemelapsed
ErmaSet-class0.310.190.53
erma-package 9.24 0.6628.53
genemodel1.440.201.64
mapmeta0.170.000.17
stateProfile 3.63 0.1021.64
states_250.000.010.02

erma.Rcheck/examples_x64/erma-Ex.timings

nameusersystemelapsed
ErmaSet-class0.400.030.44
erma-package 8.82 0.2326.55
genemodel1.470.101.57
mapmeta0.20.00.2
stateProfile 4.55 0.0824.36
states_250.000.010.01