Back to Multiple platform build/check report for BioC 3.6
ABCDEFGHIJKLMNO[P]QRSTUVWXYZ

CHECK report for Pigengene on tokay1

This page was generated on 2018-04-12 13:28:11 -0400 (Thu, 12 Apr 2018).

Package 1040/1472HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
Pigengene 1.4.20
Habil Zare
Snapshot Date: 2018-04-11 16:45:18 -0400 (Wed, 11 Apr 2018)
URL: https://git.bioconductor.org/packages/Pigengene
Branch: RELEASE_3_6
Last Commit: 7b61c56
Last Changed Date: 2018-03-18 09:41:27 -0400 (Sun, 18 Mar 2018)
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 [ WARNINGS ] OK UNNEEDED, same version exists in internal repository
veracruz1 OS X 10.11.6 El Capitan / x86_64  NotNeeded  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: Pigengene
Version: 1.4.20
Command: rm -rf Pigengene.buildbin-libdir Pigengene.Rcheck && mkdir Pigengene.buildbin-libdir Pigengene.Rcheck && C:\Users\biocbuild\bbs-3.6-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=Pigengene.buildbin-libdir Pigengene_1.4.20.tar.gz >Pigengene.Rcheck\00install.out 2>&1 && cp Pigengene.Rcheck\00install.out Pigengene-install.out && C:\Users\biocbuild\bbs-3.6-bioc\R\bin\R.exe CMD check --library=Pigengene.buildbin-libdir --install="check:Pigengene-install.out" --force-multiarch --no-vignettes --timings Pigengene_1.4.20.tar.gz
StartedAt: 2018-04-12 02:10:03 -0400 (Thu, 12 Apr 2018)
EndedAt: 2018-04-12 02:20:57 -0400 (Thu, 12 Apr 2018)
EllapsedTime: 654.4 seconds
RetCode: 0
Status:  WARNINGS  
CheckDir: Pigengene.Rcheck
Warnings: 1

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   rm -rf Pigengene.buildbin-libdir Pigengene.Rcheck && mkdir Pigengene.buildbin-libdir Pigengene.Rcheck && C:\Users\biocbuild\bbs-3.6-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=Pigengene.buildbin-libdir Pigengene_1.4.20.tar.gz >Pigengene.Rcheck\00install.out 2>&1 && cp Pigengene.Rcheck\00install.out Pigengene-install.out  &&  C:\Users\biocbuild\bbs-3.6-bioc\R\bin\R.exe CMD check --library=Pigengene.buildbin-libdir --install="check:Pigengene-install.out" --force-multiarch --no-vignettes --timings Pigengene_1.4.20.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'C:/Users/biocbuild/bbs-3.6-bioc/meat/Pigengene.Rcheck'
* using R version 3.4.4 (2018-03-15)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'Pigengene/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'Pigengene' version '1.4.20'
* 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 'Pigengene' can be installed ... WARNING
Found the following significant warnings:
  Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpueAmjg/R.INSTALL20e43ff03707/Pigengene/man/draw.bn.Rd:18: missing file link 'bn-class'
  Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpueAmjg/R.INSTALL20e43ff03707/Pigengene/man/draw.bn.Rd:67: missing file link 'bn-class'
  Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpueAmjg/R.INSTALL20e43ff03707/Pigengene/man/gene.mapping.Rd:60: missing file link 'org.Hs.eg.db'
  Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpueAmjg/R.INSTALL20e43ff03707/Pigengene/man/gene.mapping.Rd:61: missing file link 'org.Mm.eg.db'
  Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpueAmjg/R.INSTALL20e43ff03707/Pigengene/man/learn.bn.Rd:99: missing file link 'discretize'
  Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpueAmjg/R.INSTALL20e43ff03707/Pigengene/man/learn.bn.Rd:104: missing file link 'bn-class'
  Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpueAmjg/R.INSTALL20e43ff03707/Pigengene/man/learn.bn.Rd:177: missing file link 'bn-class'
See 'C:/Users/biocbuild/bbs-3.6-bioc/meat/Pigengene.Rcheck/00install.out' for details.
* 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
** 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 ... NOTE
'library' or 'require' calls in package code:
  'AnnotationDbi' 'biomaRt' 'energy' 'org.Hs.eg.db' 'org.Mm.eg.db'
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
Unexported object imported by a ':::' call: 'C50:::as.party.C5.0'
  See the note in ?`:::` about the use of this operator.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
Found the following possibly unsafe calls:
File 'Pigengene/R/bn.calculation.R':
  assignInNamespace("supported.clusters", fixArgs, "bnlearn")

check.pigengene.input: no visible global function definition for
  'setNames'
welch.pvalue: no visible global function definition for 'as.formula'
welch.pvalue: no visible global function definition for 'oneway.test'
Undefined global functions or variables:
  as.formula oneway.test setNames
Consider adding
  importFrom("stats", "as.formula", "oneway.test", "setNames")
to your NAMESPACE file.
* 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 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
one.step.pigengene 59.41   2.80   63.25
Pigengene-package  58.94   3.11   63.65
module.heatmap     20.32   0.80   21.14
compact.tree       19.03   0.10   19.16
make.decision.tree 15.22   0.16   15.37
compute.pigengene   8.92   0.15    9.23
pigengene           7.06   0.71    7.78
plot.pigengene      6.90   0.55    7.44
learn.bn            6.85   0.08    7.81
wgcna.one.step      6.03   0.08    6.11
project.eigen       5.00   0.50    5.50
** running examples for arch 'x64' ... OK
Examples with CPU or elapsed time > 5s
                    user system elapsed
Pigengene-package  54.98   2.49   58.61
one.step.pigengene 52.69   2.72   56.49
module.heatmap     18.20   0.61   18.81
make.decision.tree 15.64   0.21   15.85
compact.tree       15.61   0.06   15.69
wgcna.one.step      8.20   0.07    8.26
compute.pigengene   6.79   0.33    7.16
learn.bn            6.05   0.04    7.03
pigengene           5.54   0.45    6.00
plot.pigengene      4.99   0.50    5.48
project.eigen       4.64   0.40    5.05
* 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: 1 WARNING, 2 NOTEs
See
  'C:/Users/biocbuild/bbs-3.6-bioc/meat/Pigengene.Rcheck/00check.log'
for details.

Installation output

Pigengene.Rcheck/00install.out


install for i386

* installing *source* package 'Pigengene' ...
** R
** data
** inst
** preparing package for lazy loading
** help
*** installing help indices
  converting help for package 'Pigengene'
    finding HTML links ... done
    Pigengene-package                       html  
    aml                                     html  
    balance                                 html  
    calculate.beta                          html  
    check.nas                               html  
    check.pigengene.input                   html  
    compact.tree                            html  
    compute.pigengene                       html  
    dcor.matrix                             html  
    draw.bn                                 html  
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpueAmjg/R.INSTALL20e43ff03707/Pigengene/man/draw.bn.Rd:18: missing file link 'bn-class'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpueAmjg/R.INSTALL20e43ff03707/Pigengene/man/draw.bn.Rd:67: missing file link 'bn-class'
    eigengenes33                            html  
    gene.mapping                            html  
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpueAmjg/R.INSTALL20e43ff03707/Pigengene/man/gene.mapping.Rd:60: missing file link 'org.Hs.eg.db'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpueAmjg/R.INSTALL20e43ff03707/Pigengene/man/gene.mapping.Rd:61: missing file link 'org.Mm.eg.db'
    get.fitted.leaf                         html  
    get.genes                               html  
    get.used.features                       html  
    learn.bn                                html  
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpueAmjg/R.INSTALL20e43ff03707/Pigengene/man/learn.bn.Rd:99: missing file link 'discretize'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpueAmjg/R.INSTALL20e43ff03707/Pigengene/man/learn.bn.Rd:104: missing file link 'bn-class'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpueAmjg/R.INSTALL20e43ff03707/Pigengene/man/learn.bn.Rd:177: missing file link 'bn-class'
    make.decision.tree                      html  
    mds                                     html  
    module.heatmap                          html  
    one.step.pigengene                      html  
    pheatmap.type                           html  
    pigengene-class                         html  
    pigengene                               html  
    plot.pigengene                          html  
    preds.at                                html  
    project.eigen                           html  
    pvalues.manova                          html  
    wgcna.one.step                          html  
** building package indices
** installing vignettes
** testing if installed package can be loaded
In R CMD INSTALL

install for x64

* installing *source* package 'Pigengene' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'Pigengene' as Pigengene_1.4.20.zip
* DONE (Pigengene)
In R CMD INSTALL
In R CMD INSTALL

Tests output

Example timings

Pigengene.Rcheck/examples_i386/Pigengene-Ex.timings

nameusersystemelapsed
Pigengene-package58.94 3.1163.65
aml0.190.000.18
balance0.360.100.46
calculate.beta3.140.033.17
check.nas0.060.000.06
check.pigengene.input0.050.010.06
compact.tree19.03 0.1019.16
compute.pigengene8.920.159.23
dcor.matrix0.250.000.25
draw.bn000
eigengenes330.120.000.13
gene.mapping1.740.041.80
get.fitted.leaf0.940.061.00
get.genes0.630.040.67
get.used.features0.650.050.71
learn.bn6.850.087.81
make.decision.tree15.22 0.1615.37
mds0.140.010.16
module.heatmap20.32 0.8021.14
one.step.pigengene59.41 2.8063.25
pheatmap.type0.420.000.42
pigengene7.060.717.78
plot.pigengene6.900.557.44
preds.at0.850.050.91
project.eigen5.00.55.5
pvalues.manova0.070.000.06
wgcna.one.step6.030.086.11

Pigengene.Rcheck/examples_x64/Pigengene-Ex.timings

nameusersystemelapsed
Pigengene-package54.98 2.4958.61
aml0.140.010.16
balance0.780.070.84
calculate.beta2.880.012.89
check.nas0.060.000.07
check.pigengene.input0.050.000.04
compact.tree15.61 0.0615.69
compute.pigengene6.790.337.16
dcor.matrix0.220.020.23
draw.bn000
eigengenes330.130.030.16
gene.mapping1.480.131.61
get.fitted.leaf0.610.050.65
get.genes0.600.010.63
get.used.features0.690.020.70
learn.bn6.050.047.03
make.decision.tree15.64 0.2115.85
mds0.110.010.12
module.heatmap18.20 0.6118.81
one.step.pigengene52.69 2.7256.49
pheatmap.type0.270.020.28
pigengene5.540.456.00
plot.pigengene4.990.505.48
preds.at0.750.030.78
project.eigen4.640.405.05
pvalues.manova0.030.000.03
wgcna.one.step8.200.078.26