Back to Multiple platform build/check report for BioC 3.10
ABCDEFGHIJKLMNO[P]QRSTUVWXYZ

CHECK report for pathprint on tokay1

This page was generated on 2020-04-15 12:28:06 -0400 (Wed, 15 Apr 2020).

Package 1226/1823HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
pathprint 1.16.0
Sokratis Kariotis
Snapshot Date: 2020-04-14 16:46:13 -0400 (Tue, 14 Apr 2020)
URL: https://git.bioconductor.org/packages/pathprint
Branch: RELEASE_3_10
Last Commit: 4e1d7c0
Last Changed Date: 2019-10-29 13:10:18 -0400 (Tue, 29 Oct 2019)
malbec1 Linux (Ubuntu 18.04.4 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: 1.16.0
Command: C:\Users\biocbuild\bbs-3.10-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:pathprint.install-out.txt --library=C:\Users\biocbuild\bbs-3.10-bioc\R\library --no-vignettes --timings pathprint_1.16.0.tar.gz
StartedAt: 2020-04-15 05:21:31 -0400 (Wed, 15 Apr 2020)
EndedAt: 2020-04-15 05:30:31 -0400 (Wed, 15 Apr 2020)
EllapsedTime: 539.2 seconds
RetCode: 0
Status:  OK  
CheckDir: pathprint.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   C:\Users\biocbuild\bbs-3.10-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:pathprint.install-out.txt --library=C:\Users\biocbuild\bbs-3.10-bioc\R\library --no-vignettes --timings pathprint_1.16.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'C:/Users/biocbuild/bbs-3.10-bioc/meat/pathprint.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 'pathprint/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'pathprint' version '1.16.0'
* 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 ... 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 54.20   0.78   55.25
diffPathways           49.11   2.94   54.07
consensusDistance      26.80   3.86   33.30
customCDFAnn           22.68   1.42   24.56
consensusFingerprint   21.84   1.81   25.25
pathprint-package      21.86   0.74   22.62
thresholdFingerprint   21.28   0.74   22.02
exprs2fingerprint      18.08   0.73   18.82
pluripotents.frame     15.63   0.89   16.51
platform.thresholds    12.09   0.77   12.86
** running examples for arch 'x64' ... OK
Examples with CPU or elapsed time > 5s
                        user system elapsed
single.chip.enrichment 54.28   0.89   55.18
diffPathways           44.86   1.02   45.92
consensusDistance      18.69   1.28   19.96
thresholdFingerprint   17.96   0.69   18.64
pathprint-package      17.59   0.72   18.33
exprs2fingerprint      12.86   0.72   13.58
pluripotents.frame     12.75   0.57   13.33
consensusFingerprint   12.61   0.66   13.27
customCDFAnn           12.20   0.84   13.04
platform.thresholds     9.16   0.58    9.75
* 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/pathprint.Rcheck/00check.log'
for details.



Installation output

pathprint.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O https://malbec1.bioconductor.org/BBS/3.10/bioc/src/contrib/pathprint_1.16.0.tar.gz && rm -rf pathprint.buildbin-libdir && mkdir pathprint.buildbin-libdir && C:\Users\biocbuild\bbs-3.10-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=pathprint.buildbin-libdir pathprint_1.16.0.tar.gz && C:\Users\biocbuild\bbs-3.10-bioc\R\bin\R.exe CMD INSTALL pathprint_1.16.0.zip && rm pathprint_1.16.0.tar.gz pathprint_1.16.0.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  928k  100  928k    0     0  3072k      0 --:--:-- --:--:-- --:--:-- 3104k

install for i386

* installing *source* package 'pathprint' ...
** using staged installation
** 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 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 'pathprint' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'pathprint' as pathprint_1.16.0.zip
* DONE (pathprint)
* installing to library 'C:/Users/biocbuild/bbs-3.10-bioc/R/library'
package 'pathprint' successfully unpacked and MD5 sums checked

Tests output


Example timings

pathprint.Rcheck/examples_i386/pathprint-Ex.timings

nameusersystemelapsed
consensusDistance26.80 3.8633.30
consensusFingerprint21.84 1.8125.25
customCDFAnn22.68 1.4224.56
diffPathways49.11 2.9454.07
exprs2fingerprint18.08 0.7318.82
genesets000
pathprint-package21.86 0.7422.62
pathprint.Ce.gs0.050.020.06
pathprint.Dm.gs0.070.000.08
pathprint.Dr.gs0.130.060.19
pathprint.Hs.gs0.030.000.03
pathprint.Mm.gs0.130.100.22
pathprint.Rn.gs0.120.100.23
platform.thresholds12.09 0.7712.86
pluripotents.frame15.63 0.8916.51
single.chip.enrichment54.20 0.7855.25
thresholdFingerprint21.28 0.7422.02

pathprint.Rcheck/examples_x64/pathprint-Ex.timings

nameusersystemelapsed
consensusDistance18.69 1.2819.96
consensusFingerprint12.61 0.6613.27
customCDFAnn12.20 0.8413.04
diffPathways44.86 1.0245.92
exprs2fingerprint12.86 0.7213.58
genesets000
pathprint-package17.59 0.7218.33
pathprint.Ce.gs0.020.040.06
pathprint.Dm.gs0.010.050.07
pathprint.Dr.gs0.110.050.16
pathprint.Hs.gs0.030.000.03
pathprint.Mm.gs0.110.090.20
pathprint.Rn.gs0.110.080.19
platform.thresholds9.160.589.75
pluripotents.frame12.75 0.5713.33
single.chip.enrichment54.28 0.8955.18
thresholdFingerprint17.96 0.6918.64