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CHECK report for Pigengene on tokay2

This page was generated on 2018-10-17 08:42:22 -0400 (Wed, 17 Oct 2018).

Package 1097/1561HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
Pigengene 1.6.0
Habil Zare
Snapshot Date: 2018-10-15 16:45:08 -0400 (Mon, 15 Oct 2018)
URL: https://git.bioconductor.org/packages/Pigengene
Branch: RELEASE_3_7
Last Commit: f0c7998
Last Changed Date: 2018-04-30 10:35:42 -0400 (Mon, 30 Apr 2018)
malbec2 Linux (Ubuntu 16.04.1 LTS) / x86_64  OK  OK  WARNINGS UNNEEDED, same version exists in internal repository
tokay2 Windows Server 2012 R2 Standard / x64  OK  OK [ WARNINGS ] OK UNNEEDED, same version exists in internal repository
merida2 OS X 10.11.6 El Capitan / x86_64  OK  OK  WARNINGS  OK UNNEEDED, same version exists in internal repository

Summary

Package: Pigengene
Version: 1.6.0
Command: C:\Users\biocbuild\bbs-3.7-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:Pigengene.install-out.txt --library=C:\Users\biocbuild\bbs-3.7-bioc\R\library --no-vignettes --timings Pigengene_1.6.0.tar.gz
StartedAt: 2018-10-17 03:59:11 -0400 (Wed, 17 Oct 2018)
EndedAt: 2018-10-17 04:10:04 -0400 (Wed, 17 Oct 2018)
EllapsedTime: 653.0 seconds
RetCode: 0
Status:  WARNINGS  
CheckDir: Pigengene.Rcheck
Warnings: 2

Command output

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###
### Running command:
###
###   C:\Users\biocbuild\bbs-3.7-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:Pigengene.install-out.txt --library=C:\Users\biocbuild\bbs-3.7-bioc\R\library --no-vignettes --timings Pigengene_1.6.0.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.7-bioc/meat/Pigengene.Rcheck'
* using R version 3.5.1 Patched (2018-07-24 r75005)
* 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 '1.6.0'
* 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-3.7-bioc/tmpdir/Rtmpiw4AnA/R.INSTALL24fc389969e9/Pigengene/man/Pigengene-package.Rd:55: missing file link 'WGCNA-package'
  Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/Rtmpiw4AnA/R.INSTALL24fc389969e9/Pigengene/man/calculate.beta.Rd:8: missing file link 'WGCNA-package'
  Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/Rtmpiw4AnA/R.INSTALL24fc389969e9/Pigengene/man/calculate.beta.Rd:58: missing file link 'WGCNA-package'
  Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/Rtmpiw4AnA/R.INSTALL24fc389969e9/Pigengene/man/compute.pigengene.Rd:74: missing file link 'WGCNA-package'
  Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/Rtmpiw4AnA/R.INSTALL24fc389969e9/Pigengene/man/draw.bn.Rd:18: file link 'bn-class' in package 'bnlearn' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/Rtmpiw4AnA/R.INSTALL24fc389969e9/Pigengene/man/draw.bn.Rd:67: file link 'bn-class' in package 'bnlearn' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/Rtmpiw4AnA/R.INSTALL24fc389969e9/Pigengene/man/gene.mapping.Rd:60: file link 'org.Hs.eg.db' in package 'org.Hs.eg.db' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/Rtmpiw4AnA/R.INSTALL24fc389969e9/Pigengene/man/gene.mapping.Rd:61: file link 'org.Mm.eg.db' in package 'org.Mm.eg.db' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/Rtmpiw4AnA/R.INSTALL24fc389969e9/Pigengene/man/learn.bn.Rd:99: file link 'discretize' in package 'bnlearn' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/Rtmpiw4AnA/R.INSTALL24fc389969e9/Pigengene/man/learn.bn.Rd:104: file link 'bn-class' in package 'bnlearn' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/Rtmpiw4AnA/R.INSTALL24fc389969e9/Pigengene/man/learn.bn.Rd:177: file link 'bn-class' in package 'bnlearn' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/Rtmpiw4AnA/R.INSTALL24fc389969e9/Pigengene/man/learn.bn.Rd:202: missing file link 'WGCNA-package'
  Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/Rtmpiw4AnA/R.INSTALL24fc389969e9/Pigengene/man/one.step.pigengene.Rd:154: missing file link 'WGCNA-package'
  Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/Rtmpiw4AnA/R.INSTALL24fc389969e9/Pigengene/man/wgcna.one.step.Rd:83: missing file link 'WGCNA-package'
See 'C:/Users/biocbuild/bbs-3.7-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
* 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:
  '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.
':::' call which should be '::': '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 ... WARNING
Missing link or links in documentation object 'Pigengene-package.Rd':
  '[WGCNA]{WGCNA-package}'

Missing link or links in documentation object 'calculate.beta.Rd':
  '[WGCNA]{WGCNA-package}'

Missing link or links in documentation object 'compute.pigengene.Rd':
  '[WGCNA]{WGCNA-package}'

Missing link or links in documentation object 'learn.bn.Rd':
  '[WGCNA]{WGCNA-package}'

Missing link or links in documentation object 'one.step.pigengene.Rd':
  '[WGCNA]{WGCNA-package}'

Missing link or links in documentation object 'wgcna.one.step.Rd':
  '[WGCNA]{WGCNA-package}'

See section 'Cross-references' in the 'Writing R Extensions' manual.

* 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
one.step.pigengene 72.93   2.75   76.64
Pigengene-package  67.31   4.27   72.90
module.heatmap     21.25   0.59   21.84
compact.tree       19.41   0.14   19.63
make.decision.tree 18.19   0.18   18.38
compute.pigengene   9.24   0.31    9.62
wgcna.one.step      8.28   0.05    8.34
pigengene           6.77   0.67    7.44
plot.pigengene      6.61   0.47    7.08
learn.bn            6.00   0.04    6.92
project.eigen       4.94   0.31    5.25
** running examples for arch 'x64' ... OK
Examples with CPU or elapsed time > 5s
                    user system elapsed
Pigengene-package  54.96   2.03   60.56
one.step.pigengene 47.32   2.26   50.40
module.heatmap     17.48   0.47   18.19
make.decision.tree 13.56   0.12   13.69
compact.tree       12.80   0.04   13.69
wgcna.one.step      9.86   0.03    9.89
compute.pigengene   5.85   0.22    6.54
plot.pigengene      5.19   0.45    5.64
pigengene           4.84   0.41    5.29
learn.bn            4.47   0.05    5.53
* 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 WARNINGs, 2 NOTEs
See
  'C:/Users/biocbuild/bbs-3.7-bioc/meat/Pigengene.Rcheck/00check.log'
for details.



Installation output

Pigengene.Rcheck/00install.out

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###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O https://malbec2.bioconductor.org/BBS/3.7/bioc/src/contrib/Pigengene_1.6.0.tar.gz && rm -rf Pigengene.buildbin-libdir && mkdir Pigengene.buildbin-libdir && C:\Users\biocbuild\bbs-3.7-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=Pigengene.buildbin-libdir Pigengene_1.6.0.tar.gz && C:\Users\biocbuild\bbs-3.7-bioc\R\bin\R.exe CMD INSTALL Pigengene_1.6.0.zip && rm Pigengene_1.6.0.tar.gz Pigengene_1.6.0.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 2452k  100 2452k    0     0  29.6M      0 --:--:-- --:--:-- --:--:-- 32.3M

install for i386

* installing *source* package 'Pigengene' ...
** R
** data
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
  converting help for package 'Pigengene'
    finding HTML links ... done
    Pigengene-package                       html  
Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/Rtmpiw4AnA/R.INSTALL24fc389969e9/Pigengene/man/Pigengene-package.Rd:55: missing file link 'WGCNA-package'
    aml                                     html  
    balance                                 html  
    calculate.beta                          html  
Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/Rtmpiw4AnA/R.INSTALL24fc389969e9/Pigengene/man/calculate.beta.Rd:8: missing file link 'WGCNA-package'
Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/Rtmpiw4AnA/R.INSTALL24fc389969e9/Pigengene/man/calculate.beta.Rd:58: missing file link 'WGCNA-package'
    check.nas                               html  
    check.pigengene.input                   html  
    compact.tree                            html  
    compute.pigengene                       html  
Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/Rtmpiw4AnA/R.INSTALL24fc389969e9/Pigengene/man/compute.pigengene.Rd:74: missing file link 'WGCNA-package'
    dcor.matrix                             html  
    draw.bn                                 html  
Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/Rtmpiw4AnA/R.INSTALL24fc389969e9/Pigengene/man/draw.bn.Rd:18: file link 'bn-class' in package 'bnlearn' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/Rtmpiw4AnA/R.INSTALL24fc389969e9/Pigengene/man/draw.bn.Rd:67: file link 'bn-class' in package 'bnlearn' does not exist and so has been treated as a topic
    eigengenes33                            html  
    gene.mapping                            html  
Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/Rtmpiw4AnA/R.INSTALL24fc389969e9/Pigengene/man/gene.mapping.Rd:60: file link 'org.Hs.eg.db' in package 'org.Hs.eg.db' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/Rtmpiw4AnA/R.INSTALL24fc389969e9/Pigengene/man/gene.mapping.Rd:61: file link 'org.Mm.eg.db' in package 'org.Mm.eg.db' does not exist and so has been treated as a topic
    get.fitted.leaf                         html  
    get.genes                               html  
    get.used.features                       html  
    learn.bn                                html  
Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/Rtmpiw4AnA/R.INSTALL24fc389969e9/Pigengene/man/learn.bn.Rd:99: file link 'discretize' in package 'bnlearn' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/Rtmpiw4AnA/R.INSTALL24fc389969e9/Pigengene/man/learn.bn.Rd:104: file link 'bn-class' in package 'bnlearn' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/Rtmpiw4AnA/R.INSTALL24fc389969e9/Pigengene/man/learn.bn.Rd:177: file link 'bn-class' in package 'bnlearn' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/Rtmpiw4AnA/R.INSTALL24fc389969e9/Pigengene/man/learn.bn.Rd:202: missing file link 'WGCNA-package'
    make.decision.tree                      html  
    mds                                     html  
    module.heatmap                          html  
    one.step.pigengene                      html  
Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/Rtmpiw4AnA/R.INSTALL24fc389969e9/Pigengene/man/one.step.pigengene.Rd:154: missing file link 'WGCNA-package'
    pheatmap.type                           html  
    pigengene-class                         html  
    pigengene                               html  
    plot.pigengene                          html  
    preds.at                                html  
    project.eigen                           html  
    pvalues.manova                          html  
    wgcna.one.step                          html  
Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/Rtmpiw4AnA/R.INSTALL24fc389969e9/Pigengene/man/wgcna.one.step.Rd:83: missing file link 'WGCNA-package'
** 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_1.6.0.zip
* DONE (Pigengene)
In R CMD INSTALL
In R CMD INSTALL
* installing to library 'C:/Users/biocbuild/bbs-3.7-bioc/R/library'
package 'Pigengene' successfully unpacked and MD5 sums checked
In R CMD INSTALL

Tests output


Example timings

Pigengene.Rcheck/examples_i386/Pigengene-Ex.timings

nameusersystemelapsed
Pigengene-package67.31 4.2772.90
aml0.190.000.19
balance0.470.090.56
calculate.beta3.530.053.58
check.nas0.090.000.09
check.pigengene.input0.090.010.11
compact.tree19.41 0.1419.63
compute.pigengene9.240.319.62
dcor.matrix0.250.020.27
draw.bn000
eigengenes330.210.000.22
gene.mapping1.680.221.89
get.fitted.leaf1.030.051.08
get.genes0.890.060.95
get.used.features0.920.081.00
learn.bn6.000.046.92
make.decision.tree18.19 0.1818.38
mds0.170.010.18
module.heatmap21.25 0.5921.84
one.step.pigengene72.93 2.7576.64
pheatmap.type0.230.040.27
pigengene6.770.677.44
plot.pigengene6.610.477.08
preds.at0.760.010.78
project.eigen4.940.315.25
pvalues.manova0.060.000.06
wgcna.one.step8.280.058.34

Pigengene.Rcheck/examples_x64/Pigengene-Ex.timings

nameusersystemelapsed
Pigengene-package54.96 2.0360.56
aml0.170.000.17
balance0.500.090.59
calculate.beta3.190.023.21
check.nas0.050.000.04
check.pigengene.input0.040.000.05
compact.tree12.80 0.0413.69
compute.pigengene5.850.226.54
dcor.matrix0.260.000.27
draw.bn000
eigengenes330.20.00.2
gene.mapping1.130.121.25
get.fitted.leaf0.690.050.73
get.genes0.700.030.74
get.used.features0.560.030.59
learn.bn4.470.055.53
make.decision.tree13.56 0.1213.69
mds0.130.020.14
module.heatmap17.48 0.4718.19
one.step.pigengene47.32 2.2650.40
pheatmap.type0.230.020.25
pigengene4.840.415.29
plot.pigengene5.190.455.64
preds.at0.630.050.67
project.eigen4.560.394.95
pvalues.manova0.060.000.06
wgcna.one.step9.860.039.89