BioC 3.3: CHECK report for maSigPro on oaxaca

Package: maSigPro

Version: 1.44.0

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings maSigPro_1.44.0.tar.gz

StartedAt: 2016-10-13 03:19:53 -0700 (Thu, 13 Oct 2016)

EndedAt: 2016-10-13 03:21:24 -0700 (Thu, 13 Oct 2016)

EllapsedTime: 91.0 seconds

RetCode: 0

Status:  OK

CheckDir: maSigPro.Rcheck

Warnings: 0

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### Running command:
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###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings maSigPro_1.44.0.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.3-bioc/meat/maSigPro.Rcheck’
* using R version 3.3.1 (2016-06-21)
* using platform: x86_64-apple-darwin13.4.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘maSigPro/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘maSigPro’ version ‘1.44.0’
* 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 for sufficient/correct file permissions ... OK
* checking whether package ‘maSigPro’ 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:
  ‘Biobase’ ‘stats’ ‘MASS’
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
* 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
Namespace in Imports field not imported from: ‘utils’
  All declared Imports should be used.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
see.genes: warning in mfuzz(signif, c = k, m = m): partial argument
  match of 'c' to 'centers'
T.fit: no visible global function definition for ‘gaussian’
T.fit: no visible global function definition for ‘glm’
T.fit: no visible global function definition for ‘anova’
p.vector: no visible global function definition for ‘gaussian’
p.vector: no visible global function definition for ‘glm’
p.vector: no visible global function definition for ‘anova’
stepback: no visible global function definition for ‘gaussian’
stepback: no visible global function definition for ‘glm’
stepfor: no visible global function definition for ‘gaussian’
stepfor: no visible global function definition for ‘glm’
two.ways.stepback: no visible global function definition for ‘gaussian’
two.ways.stepback: no visible global function definition for ‘glm’
two.ways.stepfor: no visible global function definition for ‘gaussian’
two.ways.stepfor: no visible global function definition for ‘glm’
Undefined global functions or variables:
  anova gaussian glm
Consider adding
  importFrom("stats", "anova", "gaussian", "glm")
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 sizes of PDF files under ‘inst/doc’ ... OK
* checking installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU or elapsed time > 5s
              user system elapsed
T.fit        9.940  0.680  10.541
maSigPro     6.048  0.421  17.762
get.siggenes 4.733  0.328   5.024
* 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
  ‘/Users/biocbuild/bbs-3.3-bioc/meat/maSigPro.Rcheck/00check.log’
for details.

* installing *source* package ‘maSigPro’ ...
** R
** data
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (maSigPro)

name	user	system	elapsed
NBdata	0.022	0.005	0.026
NBdesign	0.002	0.001	0.003
PlotGroups	0.034	0.002	0.036
PlotProfiles	0.014	0.001	0.016
T.fit	9.940	0.680	10.541
average.rows	0.01	0.00	0.01
data.abiotic	0.005	0.001	0.006
edesign.OD	0.002	0.001	0.002
edesign.abiotic	0.004	0.002	0.028
edesignCT	0.002	0.001	0.003
edesignDR	0.002	0.001	0.003
get.siggenes	4.733	0.328	5.024
i.rank	0.001	0.000	0.001
maSigPro	6.048	0.421	17.762
maSigProUsersGuide	0.005	0.001	0.007
make.design.matrix	0.011	0.006	0.063
p.vector	2.996	0.211	3.192
position	0.001	0.000	0.001
reg.coeffs	0.001	0.001	0.001
see.genes	1.066	0.153	4.373
stepback	0.039	0.003	0.042
stepfor	0.182	0.011	0.191
suma2Venn	0.007	0.002	0.349
two.ways.stepback	0.136	0.009	0.144
two.ways.stepfor	0.184	0.011	0.192