Package: erma

Version: 1.2.0

Command: C:\Users\biocbuild\bbs-3.10-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:erma.install-out.txt --library=C:\Users\biocbuild\bbs-3.10-bioc\R\library --no-vignettes --timings erma_1.2.0.tar.gz

StartedAt: 2020-04-15 02:59:20 -0400 (Wed, 15 Apr 2020)

EndedAt: 2020-04-15 03:10:03 -0400 (Wed, 15 Apr 2020)

EllapsedTime: 643.4 seconds

RetCode: 0

Status:  OK

CheckDir: erma.Rcheck

Warnings: 0

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### Running command:
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###   C:\Users\biocbuild\bbs-3.10-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:erma.install-out.txt --library=C:\Users\biocbuild\bbs-3.10-bioc\R\library --no-vignettes --timings erma_1.2.0.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.10-bioc/meat/erma.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 'erma/DESCRIPTION' ... OK
* this is package 'erma' version '1.2.0'
* 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 199.1Mb
  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 or elapsed time > 5s
              user system elapsed
erma-package 11.28   0.74   28.53
stateProfile  3.54   0.10   23.69
** running examples for arch 'x64' ... OK
Examples with CPU or elapsed time > 5s
             user system elapsed
erma-package 9.53   0.27   33.37
stateProfile 3.88   0.06   27.53
* 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-3.10-bioc/meat/erma.Rcheck/00check.log'
for details.

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###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O https://malbec1.bioconductor.org/BBS/3.10/bioc/src/contrib/erma_1.2.0.tar.gz && rm -rf erma.buildbin-libdir && mkdir erma.buildbin-libdir && C:\Users\biocbuild\bbs-3.10-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=erma.buildbin-libdir erma_1.2.0.tar.gz && C:\Users\biocbuild\bbs-3.10-bioc\R\bin\R.exe CMD INSTALL erma_1.2.0.zip && rm erma_1.2.0.tar.gz erma_1.2.0.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
  0  197M    0     0    0     0      0      0 --:--:-- --:--:-- --:--:--     0
 10  197M   10 21.4M    0     0  19.7M      0  0:00:09  0:00:01  0:00:08 19.8M
 34  197M   34 67.7M    0     0  32.0M      0  0:00:06  0:00:02  0:00:04 32.1M
 76  197M   76  150M    0     0  48.6M      0  0:00:04  0:00:03  0:00:01 48.6M
100  197M  100  197M    0     0  54.0M      0  0:00:03  0:00:03 --:--:-- 54.1M

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_1.2.0.zip
* DONE (erma)
* installing to library 'C:/Users/biocbuild/bbs-3.10-bioc/R/library'
package 'erma' successfully unpacked and MD5 sums checked