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CHECK report for pathprint on tokay1

This page was generated on 2019-04-13 11:27:38 -0400 (Sat, 13 Apr 2019).

Package 1124/1649HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
pathprint 1.12.0
Sokratis Kariotis
Snapshot Date: 2019-04-12 17:01:30 -0400 (Fri, 12 Apr 2019)
URL: https://git.bioconductor.org/packages/pathprint
Branch: RELEASE_3_8
Last Commit: fbeb22a
Last Changed Date: 2018-10-30 11:42:04 -0400 (Tue, 30 Oct 2018)
malbec1 Linux (Ubuntu 16.04.6 LTS) / x86_64  OK  OK  OK UNNEEDED, same version exists in internal repository
tokay1 Windows Server 2012 R2 Standard / x64  OK  OK [ OK ] OK UNNEEDED, same version exists in internal repository
merida1 OS X 10.11.6 El Capitan / x86_64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: pathprint
Version: 1.12.0
Command: C:\Users\biocbuild\bbs-3.8-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:pathprint.install-out.txt --library=C:\Users\biocbuild\bbs-3.8-bioc\R\library --no-vignettes --timings pathprint_1.12.0.tar.gz
StartedAt: 2019-04-13 04:24:38 -0400 (Sat, 13 Apr 2019)
EndedAt: 2019-04-13 04:33:45 -0400 (Sat, 13 Apr 2019)
EllapsedTime: 546.9 seconds
RetCode: 0
Status:  OK  
CheckDir: pathprint.Rcheck
Warnings: 0

Command output

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###
### Running command:
###
###   C:\Users\biocbuild\bbs-3.8-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:pathprint.install-out.txt --library=C:\Users\biocbuild\bbs-3.8-bioc\R\library --no-vignettes --timings pathprint_1.12.0.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.8-bioc/meat/pathprint.Rcheck'
* using R version 3.5.3 (2019-03-11)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'pathprint/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'pathprint' version '1.12.0'
* package encoding: UTF-8
* checking package namespace information ... OK
* checking package dependencies ...Warning: unable to access index for repository https://CRAN.R-project.org/src/contrib:
  cannot open URL 'https://CRAN.R-project.org/src/contrib/PACKAGES'
 OK
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for hidden files and directories ... NOTE
Found the following hidden files and directories:
  .BBSoptions
These were most likely included in error. See section 'Package
structure' in the 'Writing R Extensions' manual.
* checking for portable file names ... OK
* checking whether package 'pathprint' 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 ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
exprs2fingerprint: no visible binding for global variable 'chipframe'
exprs2fingerprint: no visible binding for global variable 'genesets'
thresholdFingerprint: no visible binding for global variable
  'platform.thresholds'
Undefined global functions or variables:
  chipframe genesets platform.thresholds
* 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
single.chip.enrichment 49.76   2.13   51.89
diffPathways           38.20   0.92   39.12
consensusDistance      24.09   3.21   27.45
pathprint-package      22.99   1.16   24.14
consensusFingerprint   19.42   1.85   21.53
pluripotents.frame     18.27   1.09   19.38
thresholdFingerprint   18.14   0.61   18.75
exprs2fingerprint      15.61   0.92   16.55
customCDFAnn           15.53   0.54   16.08
platform.thresholds    11.51   0.61   12.14
** running examples for arch 'x64' ... OK
Examples with CPU or elapsed time > 5s
                        user system elapsed
single.chip.enrichment 56.05   0.71   56.77
diffPathways           33.53   0.62   34.15
consensusDistance      19.42   1.09   20.52
pathprint-package      17.91   0.95   18.86
thresholdFingerprint   17.62   0.73   18.36
consensusFingerprint   13.50   0.85   14.34
pluripotents.frame     13.20   0.84   14.05
customCDFAnn           12.89   0.53   13.43
exprs2fingerprint      12.33   0.55   12.88
platform.thresholds     9.23   0.59    9.83
* 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-3.8-bioc/meat/pathprint.Rcheck/00check.log'
for details.



Installation output

pathprint.Rcheck/00install.out

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###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O https://malbec1.bioconductor.org/BBS/3.8/bioc/src/contrib/pathprint_1.12.0.tar.gz && rm -rf pathprint.buildbin-libdir && mkdir pathprint.buildbin-libdir && C:\Users\biocbuild\bbs-3.8-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=pathprint.buildbin-libdir pathprint_1.12.0.tar.gz && C:\Users\biocbuild\bbs-3.8-bioc\R\bin\R.exe CMD INSTALL pathprint_1.12.0.zip && rm pathprint_1.12.0.tar.gz pathprint_1.12.0.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
100  928k  100  928k    0     0  19.0M      0 --:--:-- --:--:-- --:--:-- 20.6M

install for i386

* installing *source* package 'pathprint' ...
** R
** data
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
  converting help for package 'pathprint'
    finding HTML links ... done
    consensusDistance                       html  
    consensusFingerprint                    html  
    customCDFAnn                            html  
    diffPathways                            html  
    exprs2fingerprint                       html  
    genesets                                html  
    pathprint-package                       html  
    pathprint.Ce.gs                         html  
    pathprint.Dm.gs                         html  
    pathprint.Dr.gs                         html  
    pathprint.Hs.gs                         html  
    pathprint.Mm.gs                         html  
    pathprint.Rn.gs                         html  
    platform.thresholds                     html  
    pluripotents.frame                      html  
    single.chip.enrichment                  html  
    thresholdFingerprint                    html  
** building package indices
** installing vignettes
** testing if installed package can be loaded
In R CMD INSTALL

install for x64

* installing *source* package 'pathprint' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'pathprint' as pathprint_1.12.0.zip
* DONE (pathprint)
In R CMD INSTALL
In R CMD INSTALL
* installing to library 'C:/Users/biocbuild/bbs-3.8-bioc/R/library'
package 'pathprint' successfully unpacked and MD5 sums checked
In R CMD INSTALL

Tests output


Example timings

pathprint.Rcheck/examples_i386/pathprint-Ex.timings

nameusersystemelapsed
consensusDistance24.09 3.2127.45
consensusFingerprint19.42 1.8521.53
customCDFAnn15.53 0.5416.08
diffPathways38.20 0.9239.12
exprs2fingerprint15.61 0.9216.55
genesets000
pathprint-package22.99 1.1624.14
pathprint.Ce.gs0.050.010.08
pathprint.Dm.gs0.050.030.10
pathprint.Dr.gs0.110.130.25
pathprint.Hs.gs0.040.000.04
pathprint.Mm.gs0.130.170.33
pathprint.Rn.gs0.080.220.31
platform.thresholds11.51 0.6112.14
pluripotents.frame18.27 1.0919.38
single.chip.enrichment49.76 2.1351.89
thresholdFingerprint18.14 0.6118.75

pathprint.Rcheck/examples_x64/pathprint-Ex.timings

nameusersystemelapsed
consensusDistance19.42 1.0920.52
consensusFingerprint13.50 0.8514.34
customCDFAnn12.89 0.5313.43
diffPathways33.53 0.6234.15
exprs2fingerprint12.33 0.5512.88
genesets000
pathprint-package17.91 0.9518.86
pathprint.Ce.gs0.000.050.05
pathprint.Dm.gs0.030.030.06
pathprint.Dr.gs0.080.050.13
pathprint.Hs.gs0.030.000.03
pathprint.Mm.gs0.090.060.15
pathprint.Rn.gs0.070.100.16
platform.thresholds9.230.599.83
pluripotents.frame13.20 0.8414.05
single.chip.enrichment56.05 0.7156.77
thresholdFingerprint17.62 0.7318.36