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).
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 | |  |
| tokay1 | Windows Server 2012 R2 Standard / x64 | NotNeeded | OK | [ OK ] | OK | |
| morelia | Mac OS X Mavericks (10.9.5) / x86_64 | NotNeeded | OK | OK | OK | |
Summary
| Package: recount
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| Version: 1.0.17
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| 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
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| StartedAt: 2017-04-15 00:25:43 -0400 (Sat, 15 Apr 2017)
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| EndedAt: 2017-04-15 00:47:17 -0400 (Sat, 15 Apr 2017)
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| EllapsedTime: 1293.4 seconds
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| RetCode: 0
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| Status: OK
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| CheckDir: recount.Rcheck
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| Warnings: 0
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Command output
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### 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
###
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* 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:
| name | user | system | elapsed
|
| abstract_search | 0.22 | 0.00 | 0.22 |
|
| all_metadata | 0.96 | 0.03 | 2.01 |
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| browse_study | 0.19 | 0.00 | 0.19 |
|
| coverage_matrix | 0 | 0 | 0 |
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| download_study | 2.33 | 0.08 | 3.23 |
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| expressed_regions | 0 | 0 | 0 |
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| find_geo | 0.31 | 0.17 | 1.58 |
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| geo_characteristics | 0.32 | 0.01 | 3.91 |
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| geo_info | 0.09 | 0.00 | 0.09 |
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| reproduce_ranges | 130.87 | 9.80 | 145.02 |
|
| scale_counts | 0.41 | 0.00 | 0.41 |
|
| snaptron_query | 0.54 | 0.02 | 6.08 |
|
recount.Rcheck/examples_x64/recount-Ex.timings:
| name | user | system | elapsed
|
| abstract_search | 0.28 | 0.00 | 0.28 |
|
| all_metadata | 1.62 | 0.06 | 2.44 |
|
| browse_study | 0.16 | 0.00 | 0.16 |
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| coverage_matrix | 0 | 0 | 0 |
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| download_study | 2.79 | 0.05 | 3.53 |
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| expressed_regions | 0 | 0 | 0 |
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| find_geo | 0.27 | 0.07 | 1.43 |
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| geo_characteristics | 0.30 | 0.05 | 4.15 |
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| geo_info | 0.12 | 0.00 | 0.12 |
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| reproduce_ranges | 144.36 | 6.27 | 154.56 |
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| scale_counts | 0.25 | 0.00 | 0.25 |
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| snaptron_query | 2.33 | 0.07 | 8.17 |
|