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CHECK report for PCpheno on tokay2

This page was generated on 2020-10-17 11:57:22 -0400 (Sat, 17 Oct 2020).

TO THE DEVELOPERS/MAINTAINERS OF THE PCpheno PACKAGE: Please make sure to use the following settings in order to reproduce any error or warning you see on this page.
Package 1286/1905HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
PCpheno 1.50.0
Nolwenn Le Meur
Snapshot Date: 2020-10-16 14:40:19 -0400 (Fri, 16 Oct 2020)
URL: https://git.bioconductor.org/packages/PCpheno
Branch: RELEASE_3_11
Last Commit: 9428ada
Last Changed Date: 2020-04-27 14:16:21 -0400 (Mon, 27 Apr 2020)
malbec2 Linux (Ubuntu 18.04.4 LTS) / x86_64  OK  OK  OK UNNEEDED, same version exists in internal repository
tokay2 Windows Server 2012 R2 Standard / x64  OK  OK [ OK ] OK UNNEEDED, same version exists in internal repository
machv2 macOS 10.14.6 Mojave / x86_64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: PCpheno
Version: 1.50.0
Command: C:\Users\biocbuild\bbs-3.11-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:PCpheno.install-out.txt --library=C:\Users\biocbuild\bbs-3.11-bioc\R\library --no-vignettes --timings PCpheno_1.50.0.tar.gz
StartedAt: 2020-10-17 06:47:33 -0400 (Sat, 17 Oct 2020)
EndedAt: 2020-10-17 06:52:22 -0400 (Sat, 17 Oct 2020)
EllapsedTime: 288.9 seconds
RetCode: 0
Status:  OK  
CheckDir: PCpheno.Rcheck
Warnings: 0

Command output

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###
### Running command:
###
###   C:\Users\biocbuild\bbs-3.11-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:PCpheno.install-out.txt --library=C:\Users\biocbuild\bbs-3.11-bioc\R\library --no-vignettes --timings PCpheno_1.50.0.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.11-bioc/meat/PCpheno.Rcheck'
* using R version 4.0.3 (2020-10-10)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'PCpheno/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'PCpheno' version '1.50.0'
* checking package namespace information ... OK
* checking package dependencies ... NOTE
Depends: includes the non-default packages:
  'Category', 'ScISI', 'SLGI', 'ppiStats', 'ppiData', 'annotate'
Adding so many packages to the search path is excessive and importing
selectively is preferable.
* 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 'PCpheno' can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking 'build' directory ... OK
* checking DESCRIPTION meta-information ... NOTE
Packages listed in more than one of Depends, Imports, Suggests, Enhances:
  'Category' 'ScISI' 'KEGG.db' 'GO.db'
A package should be listed in only one of these fields.
* 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 ... NOTE
'library' or 'require' calls in package code:
  'GO.db' 'KEGG.db'
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
Packages in Depends field not imported from:
  'SLGI' 'annotate' 'ppiData' 'ppiStats'
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
* 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 ... 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 (user + system) or elapsed time > 5s
               user system elapsed
graphTheory    5.78   0.22     6.0
gtResult-class 4.30   0.89     5.2
** running examples for arch 'x64' ... OK
Examples with CPU (user + system) or elapsed time > 5s
               user system elapsed
graphTheory    6.94   0.28    7.23
gtResult-class 4.55   0.95    5.50
* 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: 3 NOTEs
See
  'C:/Users/biocbuild/bbs-3.11-bioc/meat/PCpheno.Rcheck/00check.log'
for details.



Installation output

PCpheno.Rcheck/00install.out

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###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O https://malbec2.bioconductor.org/BBS/3.11/bioc/src/contrib/PCpheno_1.50.0.tar.gz && rm -rf PCpheno.buildbin-libdir && mkdir PCpheno.buildbin-libdir && C:\Users\biocbuild\bbs-3.11-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=PCpheno.buildbin-libdir PCpheno_1.50.0.tar.gz && C:\Users\biocbuild\bbs-3.11-bioc\R\bin\R.exe CMD INSTALL PCpheno_1.50.0.zip && rm PCpheno_1.50.0.tar.gz PCpheno_1.50.0.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  810k  100  810k    0     0  8694k      0 --:--:-- --:--:-- --:--:-- 9311k

install for i386

* installing *source* package 'PCpheno' ...
** using staged installation
** R
** data
** byte-compile and prepare package for lazy loading
No methods found in package 'Biobase' for request: 'listlen' when loading 'RpsiXML'
No methods found in package 'annotate' for requests: 'pubmed', 'buildPubMedAbst' when loading 'RpsiXML'
No methods found in package 'BiocGenerics' for request: 'plot' when loading 'SLGI'
** help
*** installing help indices
  converting help for package 'PCpheno'
    finding HTML links ... done
    CoHyperGParams-class                    html  
    CoHyperGResult-class                    html  
    Dudley                                  html  
    Giaever                                 html  
    HI                                      html  
    KEGG2SCISI                              html  
    Kastenmayer                             html  
    Lesage                                  html  
    Osterberg                               html  
    PCpheno.package                         html  
    SGDphenoL                               html  
    YEASTOHNOLOG                            html  
    buildFDMat                              html  
    categoryToEntrezBuilder                 html  
    complexStatus                           html  
    deResult-class                          html  
    densityEstimate                         html  
    getDescr                                html  
    getFDgene                               html  
    graphTheory                             html  
    gtResult-class                          html  
    overlap                                 html  
    plot                                    html  
    ppiInteraction                          html  
    reduceM                                 html  
    testResult-class                        html  
    truncName                               html  
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
No methods found in package 'Biobase' for request: 'listlen' when loading 'RpsiXML'
No methods found in package 'annotate' for requests: 'pubmed', 'buildPubMedAbst' when loading 'RpsiXML'
No methods found in package 'BiocGenerics' for request: 'plot' when loading 'SLGI'
** testing if installed package can be loaded from final location
No methods found in package 'Biobase' for request: 'listlen' when loading 'RpsiXML'
No methods found in package 'annotate' for requests: 'pubmed', 'buildPubMedAbst' when loading 'RpsiXML'
No methods found in package 'BiocGenerics' for request: 'plot' when loading 'SLGI'
** testing if installed package keeps a record of temporary installation path

install for x64

* installing *source* package 'PCpheno' ...
** testing if installed package can be loaded
No methods found in package 'Biobase' for request: 'listlen' when loading 'RpsiXML'
No methods found in package 'annotate' for requests: 'pubmed', 'buildPubMedAbst' when loading 'RpsiXML'
No methods found in package 'BiocGenerics' for request: 'plot' when loading 'SLGI'
* MD5 sums
packaged installation of 'PCpheno' as PCpheno_1.50.0.zip
* DONE (PCpheno)
* installing to library 'C:/Users/biocbuild/bbs-3.11-bioc/R/library'
package 'PCpheno' successfully unpacked and MD5 sums checked

Tests output


Example timings

PCpheno.Rcheck/examples_i386/PCpheno-Ex.timings

nameusersystemelapsed
CoHyperGResult-class0.210.000.25
Dudley0.000.010.03
Giaever0.270.050.32
HI000
KEGG2SCISI0.100.030.30
Kastenmayer0.060.020.08
Lesage0.000.010.01
Osterberg0.030.000.03
SGDphenoL0.030.000.03
YEASTOHNOLOG0.000.020.02
buildFDMat0.220.030.25
categoryToEntrezBuilder0.090.080.20
complexStatus0.670.120.83
deResult-class0.100.030.12
densityEstimate0.760.110.88
getDescr0.920.021.03
getFDgene0.160.010.17
graphTheory5.780.226.00
gtResult-class4.300.895.20
overlap0.010.000.02
plot0.540.190.72
ppiInteraction3.120.563.84
reduceM000
truncName000

PCpheno.Rcheck/examples_x64/PCpheno-Ex.timings

nameusersystemelapsed
CoHyperGResult-class0.520.080.59
Dudley0.010.010.03
Giaever0.140.020.16
HI0.000.010.02
KEGG2SCISI0.100.020.11
Kastenmayer0.030.000.03
Lesage0.010.020.03
Osterberg0.020.010.03
SGDphenoL0.050.000.05
YEASTOHNOLOG0.010.000.01
buildFDMat0.150.030.19
categoryToEntrezBuilder0.110.030.14
complexStatus0.780.070.84
deResult-class0.080.040.12
densityEstimate0.560.190.75
getDescr0.60.00.6
getFDgene0.120.020.14
graphTheory6.940.287.23
gtResult-class4.550.955.50
overlap000
plot0.790.231.03
ppiInteraction3.470.083.55
reduceM000
truncName000