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BioC 3.4: CHECK report for recount on tokay1

This page was generated on 2017-04-15 16:21:21 -0400 (Sat, 15 Apr 2017).

Package 1026/1296HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
recount 1.0.17
Leonardo Collado-Torres
Snapshot Date: 2017-04-14 17:17:13 -0400 (Fri, 14 Apr 2017)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_3_4/madman/Rpacks/recount
Last Changed Rev: 127577 / Revision: 128728
Last Changed Date: 2017-03-21 12:44:47 -0400 (Tue, 21 Mar 2017)
malbec1 Linux (Ubuntu 16.04.1 LTS) / x86_64  NotNeeded  OK  OK UNNEEDED, same version exists in internal repository
tokay1 Windows Server 2012 R2 Standard / x64  NotNeeded  OK [ OK ] OK UNNEEDED, same version exists in internal repository
morelia Mac OS X Mavericks (10.9.5) / x86_64  NotNeeded  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: recount
Version: 1.0.17
Command: rm -rf recount.buildbin-libdir recount.Rcheck && mkdir recount.buildbin-libdir recount.Rcheck && C:\Users\biocbuild\bbs-3.4-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=recount.buildbin-libdir recount_1.0.17.tar.gz >recount.Rcheck\00install.out 2>&1 && cp recount.Rcheck\00install.out recount-install.out && C:\Users\biocbuild\bbs-3.4-bioc\R\bin\R.exe CMD check --library=recount.buildbin-libdir --install="check:recount-install.out" --force-multiarch --no-vignettes --timings recount_1.0.17.tar.gz
StartedAt: 2017-04-15 00:25:43 -0400 (Sat, 15 Apr 2017)
EndedAt: 2017-04-15 00:47:17 -0400 (Sat, 15 Apr 2017)
EllapsedTime: 1293.4 seconds
RetCode: 0
Status:  OK  
CheckDir: recount.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   rm -rf recount.buildbin-libdir recount.Rcheck && mkdir recount.buildbin-libdir recount.Rcheck && C:\Users\biocbuild\bbs-3.4-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=recount.buildbin-libdir recount_1.0.17.tar.gz >recount.Rcheck\00install.out 2>&1 && cp recount.Rcheck\00install.out recount-install.out  && C:\Users\biocbuild\bbs-3.4-bioc\R\bin\R.exe CMD check --library=recount.buildbin-libdir --install="check:recount-install.out" --force-multiarch --no-vignettes --timings recount_1.0.17.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'C:/Users/biocbuild/bbs-3.4-bioc/meat/recount.Rcheck'
* using R version 3.3.3 (2017-03-06)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'recount/DESCRIPTION' ... OK
* this is package 'recount' version '1.0.17'
* package encoding: UTF-8
* 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 'recount' can be installed ... OK
* checking installed package size ... NOTE
  installed size is 13.2Mb
  sub-directories of 1Mb or more:
    data  10.7Mb
    doc    2.4Mb
* 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
** checking loading without being on the library search path ... 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 loading without being on the library search path ... 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 ... OK
* 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 ... NOTE
  Note: found 347 marked UTF-8 strings
* checking data for ASCII and uncompressed saves ... OK
* checking line endings in Makefiles ... OK
* checking for GNU extensions in Makefiles ... OK
* checking installed files from 'inst/doc' ... OK
* checking files in 'vignettes' ... OK
* checking examples ...
** running examples for arch 'i386' ... OK
Examples with CPU or elapsed time > 5s
                   user system elapsed
reproduce_ranges 130.87   9.80  145.02
snaptron_query     0.54   0.02    6.08
** running examples for arch 'x64' ... OK
Examples with CPU or elapsed time > 5s
                   user system elapsed
reproduce_ranges 144.36   6.27  154.56
snaptron_query     2.33   0.07    8.17
* checking for unstated dependencies in 'tests' ... OK
* checking tests ...
** running tests for arch 'i386' ...
  Running 'test-all.R'
 OK
** running tests for arch 'x64' ...
  Running 'test-all.R'
 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-3.4-bioc/meat/recount.Rcheck/00check.log'
for details.


recount.Rcheck/00install.out:


install for i386

* installing *source* package 'recount' ...
** R
** data
*** moving datasets to lazyload DB
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded

install for x64

* installing *source* package 'recount' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'recount' as recount_1.0.17.zip
* DONE (recount)

recount.Rcheck/examples_i386/recount-Ex.timings:

nameusersystemelapsed
abstract_search0.220.000.22
all_metadata0.960.032.01
browse_study0.190.000.19
coverage_matrix000
download_study2.330.083.23
expressed_regions000
find_geo0.310.171.58
geo_characteristics0.320.013.91
geo_info0.090.000.09
reproduce_ranges130.87 9.80145.02
scale_counts0.410.000.41
snaptron_query0.540.026.08

recount.Rcheck/examples_x64/recount-Ex.timings:

nameusersystemelapsed
abstract_search0.280.000.28
all_metadata1.620.062.44
browse_study0.160.000.16
coverage_matrix000
download_study2.790.053.53
expressed_regions000
find_geo0.270.071.43
geo_characteristics0.300.054.15
geo_info0.120.000.12
reproduce_ranges144.36 6.27154.56
scale_counts0.250.000.25
snaptron_query2.330.078.17