Package: altcdfenvs

Version: 2.45.1

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:altcdfenvs.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings altcdfenvs_2.45.1.tar.gz

StartedAt: 2019-04-08 23:11:32 -0400 (Mon, 08 Apr 2019)

EndedAt: 2019-04-08 23:13:35 -0400 (Mon, 08 Apr 2019)

EllapsedTime: 122.9 seconds

RetCode: 0

Status:  OK

CheckDir: altcdfenvs.Rcheck

Warnings: 0

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### Running command:
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###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:altcdfenvs.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings altcdfenvs_2.45.1.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.9-bioc/meat/altcdfenvs.Rcheck’
* using R Under development (unstable) (2018-11-27 r75683)
* using platform: x86_64-apple-darwin15.6.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘altcdfenvs/DESCRIPTION’ ... OK
* this is package ‘altcdfenvs’ version ‘2.45.1’
* checking package namespace information ... OK
* checking package dependencies ... NOTE
Depends: includes the non-default packages:
  'BiocGenerics', 'S4Vectors', 'Biobase', 'affy', 'makecdfenv',
  'Biostrings', 'hypergraph'
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 for sufficient/correct file permissions ... OK
* checking whether package ‘altcdfenvs’ can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... NOTE
Malformed Description field: should contain one or more complete sentences.
* 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
Packages in Depends field not imported from:
  ‘Biobase’ ‘Biostrings’ ‘hypergraph’ ‘makecdfenv’ ‘methods’
  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 ... NOTE
Found the following apparent S3 methods exported but not registered:
  plot.CdfEnvAffy print.FASTA unique.CdfEnvAffy
See section ‘Registering S3 methods’ in the ‘Writing R Extensions’
manual.
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
buildCdfEnv.biostrings: no visible global function definition for
  ‘validObject’
buildCdfEnv.biostrings: no visible global function definition for ‘is’
buildCdfEnv.biostrings: no visible global function definition for ‘new’
buildCdfEnv.biostrings: no visible global function definition for
  ‘update’
buildCdfEnv.biostrings: no visible global function definition for
  ‘xy2indices’
buildCdfEnv.matchprobes: no visible global function definition for ‘is’
buildCdfEnv.matchprobes: no visible global function definition for
  ‘new’
buildCdfEnv.matchprobes: no visible global function definition for
  ‘update’
buildCdfEnv.matchprobes: no visible global function definition for
  ‘xy2indices’
copyCdfEnvAffy: no visible global function definition for ‘copyEnv’
countduplicated: no visible global function definition for ‘is’
countduplicated: no visible global function definition for ‘as’
geneNames.CdfEnvAffy: no visible global function definition for ‘as’
getCdfEnvAffy: no visible global function definition for ‘is’
getCdfEnvAffy: no visible global function definition for ‘getCdfInfo’
index2xy.CdfEnvAffy: no visible global function definition for
  ‘indices2xy’
indexProbes.CdfEnvAffy: no visible global function definition for ‘as’
matchAffyProbes: no visible global function definition for
  ‘DNAStringSet’
matchAffyProbes: no visible global function definition for ‘DNAString’
matchAffyProbes: no visible global function definition for ‘PDict’
matchAffyProbes: no visible global function definition for ‘matchPDict’
matchAffyProbes: no visible global function definition for ‘new’
removeIndex: no visible global function definition for ‘as’
unique.CdfEnvAffy: no visible global function definition for ‘as’
validAffyBatch: no visible global function definition for ‘is’
validCdfEnvAffy: no visible global function definition for ‘as’
wrapCdfEnvAffy: no visible global function definition for ‘new’
xy2index.CdfEnvAffy: no visible global function definition for
  ‘xy2indices’
[,CdfEnvAffy-character-missing-missing: no visible global function
  definition for ‘as’
coerce,CdfEnvAffy-Cdf: no visible global function definition for ‘new’
combine,AffyProbesMatch-AffyProbesMatch: no visible global function
  definition for ‘new’
geneNames,CdfEnvAffy: no visible global function definition for ‘as’
indexProbes,CdfEnvAffy-character: no visible global function definition
  for ‘as’
show,CdfEnvAffy: no visible global function definition for ‘as’
toHypergraph,AffyProbesMatch : <anonymous>: no visible global function
  definition for ‘Hyperedge’
toHypergraph,AffyProbesMatch: no visible global function definition for
  ‘new’
toHypergraph,CdfEnvAffy : <anonymous>: no visible global function
  definition for ‘Hyperedge’
toHypergraph,CdfEnvAffy: no visible global function definition for
  ‘new’
Undefined global functions or variables:
  DNAString DNAStringSet Hyperedge PDict as copyEnv getCdfInfo
  indices2xy is matchPDict new update validObject xy2indices
Consider adding
  importFrom("methods", "as", "is", "new", "validObject")
  importFrom("stats", "update")
to your NAMESPACE file (and ensure that your DESCRIPTION Imports field
contains 'methods').
* 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 files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU or elapsed time > 5s
                 user system elapsed
removeIndex     9.867  0.053  10.021
matchAffyProbes 6.220  0.298   6.572
* 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: 5 NOTEs
See
  ‘/Users/biocbuild/bbs-3.9-bioc/meat/altcdfenvs.Rcheck/00check.log’
for details.

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### Running command:
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###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD INSTALL altcdfenvs
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* installing to library ‘/Library/Frameworks/R.framework/Versions/3.6/Resources/library’
* installing *source* package ‘altcdfenvs’ ...
** R
** data
** inst
** byte-compile and prepare package for lazy loading
NOTE: arguments in definition for validity method for class 'AffyProbesMatch' changed from (obj) to (object)
in method for ‘toHypergraph’ with signature ‘"CdfEnvAffy"’: no definition for class “CdfEnvAffy”
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (altcdfenvs)

name	user	system	elapsed
AffyProbesMatch-class	0.001	0.000	0.001
CdfEnvAffy-class	4.017	0.087	4.139
appendCdfEnvAffy	0.005	0.002	0.007
cdfenv	0.000	0.001	0.000
cdfenvEx	0.003	0.002	0.005
getxy.probeseq	0.000	0.000	0.001
index2xy	0	0	0
matchAffyProbes	6.220	0.298	6.572
plot.CdfEnvAffy	0.001	0.000	0.000
removeIndex	9.867	0.053	10.021
unique.CdfEnvAffy	0	0	0
utils.FASTA	0.004	0.001	0.004
validAffyBatch	0.000	0.000	0.001