Package: qcmetrics

Version: 1.22.0

Command: C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:qcmetrics.install-out.txt --library=C:\Users\biocbuild\bbs-3.9-bioc\R\library --no-vignettes --timings qcmetrics_1.22.0.tar.gz

StartedAt: 2019-10-16 06:14:38 -0400 (Wed, 16 Oct 2019)

EndedAt: 2019-10-16 06:16:16 -0400 (Wed, 16 Oct 2019)

EllapsedTime: 98.0 seconds

RetCode: 0

Status:  OK

CheckDir: qcmetrics.Rcheck

Warnings: 0

##############################################################################
##############################################################################
###
### Running command:
###
###   C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:qcmetrics.install-out.txt --library=C:\Users\biocbuild\bbs-3.9-bioc\R\library --no-vignettes --timings qcmetrics_1.22.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'C:/Users/biocbuild/bbs-3.9-bioc/meat/qcmetrics.Rcheck'
* using R version 3.6.1 (2019-07-05)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'qcmetrics/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'qcmetrics' version '1.22.0'
* 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 'qcmetrics' can be installed ... OK
* checking installed package size ... OK
* 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 ... NOTE
Found the following apparent S3 methods exported but not registered:
  as.data.frame.QcMetrics
See section 'Registering S3 methods' in the 'Writing R Extensions'
manual.
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
n15qc: no visible global function definition for 'fvarLabels'
n15qc: no visible global function definition for 'fData'
n15qc : : no visible global function definition for 'ggplot'
n15qc : : no visible global function definition for 'aes'
n15qc : : no visible global function definition for
  'geom_jitter'
n15qc : : no visible global function definition for
  'geom_boxplot'
n15qc : : no visible global function definition for
  'geom_hline'
n15qc : : no visible global function definition for 'labs'
n15qc: no visible global function definition for 'fData<-'
n15qc: no visible global function definition for 'combineFeatures'
n15qc: no visible global function definition for 'exprs'
n15qc: no visible global function definition for 'fileNames'
n15qc: no visible global function definition for 'experimentData'
Undefined global functions or variables:
  aes combineFeatures experimentData exprs fData fData<- fileNames
  fvarLabels geom_boxplot geom_hline geom_jitter ggplot labs
* 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
qcReport-methods 1.09   0.19    5.07
** 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: 2 NOTEs
See
  'C:/Users/biocbuild/bbs-3.9-bioc/meat/qcmetrics.Rcheck/00check.log'
for details.

##############################################################################
##############################################################################
###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O https://malbec2.bioconductor.org/BBS/3.9/bioc/src/contrib/qcmetrics_1.22.0.tar.gz && rm -rf qcmetrics.buildbin-libdir && mkdir qcmetrics.buildbin-libdir && C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=qcmetrics.buildbin-libdir qcmetrics_1.22.0.tar.gz && C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD INSTALL qcmetrics_1.22.0.zip && rm qcmetrics_1.22.0.tar.gz qcmetrics_1.22.0.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
100 2656k  100 2656k    0     0  23.4M      0 --:--:-- --:--:-- --:--:-- 24.9M

install for i386

* installing *source* package 'qcmetrics' ...
** using staged installation
** R
** data
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
  converting help for package 'qcmetrics'
    finding HTML links ... done
    Qc2Tex                                  html  
    QcMetadata-class                        html  
    QcMetric-class                          html  
    QcMetrics-class                         html  
    finding level-2 HTML links ... done

    n15qc                                   html  
    psm                                     html  
    qcReport-methods                        html  
    rnadeg                                  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 'qcmetrics' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'qcmetrics' as qcmetrics_1.22.0.zip
* DONE (qcmetrics)
* installing to library 'C:/Users/biocbuild/bbs-3.9-bioc/R/library'
package 'qcmetrics' successfully unpacked and MD5 sums checked