Package: fCI

Version: 1.14.0

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:fCI.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings fCI_1.14.0.tar.gz

StartedAt: 2019-10-16 02:46:27 -0400 (Wed, 16 Oct 2019)

EndedAt: 2019-10-16 02:47:38 -0400 (Wed, 16 Oct 2019)

EllapsedTime: 71.2 seconds

RetCode: 0

Status:  WARNINGS

CheckDir: fCI.Rcheck

Warnings: 1

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### Running command:
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###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:fCI.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings fCI_1.14.0.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.9-bioc/meat/fCI.Rcheck’
* using R version 3.6.1 (2019-07-05)
* using platform: x86_64-apple-darwin15.6.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘fCI/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘fCI’ version ‘1.14.0’
* checking package namespace information ... OK
* checking package dependencies ... NOTE
Depends: includes the non-default packages:
  'FNN', 'psych', 'gtools', 'zoo', 'rgl', 'grid', 'VennDiagram'
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 ‘fCI’ can be installed ... WARNING
Found the following significant warnings:
  Warning: 'rgl_init' failed, running with rgl.useNULL = TRUE
See ‘/Users/biocbuild/bbs-3.9-bioc/meat/fCI.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
* 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
package 'methods' is used but not declared
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
fCI.call.by.index: no visible global function definition for ‘new’
fCI.call.by.index: no visible global function definition for
  ‘initialize’
find.fci.targets,NPCI: no visible global function definition for
  ‘initialize’
populate,NPCI: no visible global function definition for ‘.hasSlot’
populate,NPCI: no visible global function definition for ‘slot’
Undefined global functions or variables:
  .hasSlot initialize new slot
Consider adding
  importFrom("methods", ".hasSlot", "initialize", "new", "slot")
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 installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
* 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, 3 NOTEs
See
  ‘/Users/biocbuild/bbs-3.9-bioc/meat/fCI.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 fCI
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* installing to library ‘/Library/Frameworks/R.framework/Versions/3.6/Resources/library’
* installing *source* package ‘fCI’ ...
** using staged installation
** R
** data
** inst
** byte-compile and prepare package for lazy loading
Warning messages:
1: In rgl.init(initValue, onlyNULL) : RGL: GLX extension missing on server
2: 'rgl_init' failed, running with rgl.useNULL = TRUE 
in method for ‘initialize’ with signature ‘"NPCI"’: no definition for class “NPCI”
in method for ‘normalization’ with signature ‘"NPCI"’: no definition for class “NPCI”
in method for ‘setfCI’ with signature ‘"NPCI"’: no definition for class “NPCI”
in method for ‘populate’ with signature ‘"NPCI"’: no definition for class “NPCI”
in method for ‘find.fci.targets’ with signature ‘"NPCI"’: no definition for class “NPCI”
in method for ‘show.targets’ with signature ‘"NPCI"’: no definition for class “NPCI”
in method for ‘call.npci’ with signature ‘"NPCI"’: no definition for class “NPCI”
in method for ‘compute’ with signature ‘"NPCI"’: no definition for class “NPCI”
** help
*** installing help indices
** building package indices
** installing vignettes
   ‘fCI.Rmd’ 
** testing if installed package can be loaded from temporary location
Warning in rgl.init(initValue, onlyNULL) :
  RGL: GLX extension missing on server
Warning: 'rgl_init' failed, running with rgl.useNULL = TRUE
** testing if installed package can be loaded from final location
Warning in rgl.init(initValue, onlyNULL) :
  RGL: GLX extension missing on server
Warning: 'rgl_init' failed, running with rgl.useNULL = TRUE
** testing if installed package keeps a record of temporary installation path
* DONE (fCI)

name	user	system	elapsed
NPCI-class	0.003	0.001	0.005
call.npci	0	0	0
compute	0.001	0.000	0.001
deg.pairwise.fold.change	0.002	0.000	0.002
deg.up.down.info	0.000	0.000	0.001
deseq.median.ratio.normalization	0.016	0.004	0.020
divergence.multivariate.distributions	0.012	0.004	0.015
fCI-class	0.004	0.002	0.005
fCI.call.by.index	2.314	0.428	2.747
figures	0.000	0.001	0.001
find.fci.targets	4.564	0.348	4.914
find.mid.point	0.611	0.059	0.670
get.fold.large.step	0.001	0.000	0.001
get.npci.data	0.003	0.004	0.006
get.npci.distance.matrix	0.045	0.003	0.049
get.outline.index	0.007	0.001	0.007
get.protein.fold.step	0.001	0.000	0.000
get.rank.combinations	0.002	0.000	0.003
get.rna.fold.step	0.001	0.000	0.002
intersect.of.lists	0.000	0.000	0.001
is.installed	0.042	0.001	0.043
normalization	0.001	0.001	0.001
npci.gene.by.pvalues	0.014	0.001	0.014
npci.index.reconsidered	0.142	0.003	0.144
npci.index.to.be.removed	0	0	0
npci.venn.diagram	0.223	0.042	0.278
pairwise.change.occupancy	0.002	0.001	0.002
populate	0.001	0.000	0.001
report.target.summary	0.000	0.001	0.000
setfCI	0.001	0.000	0.001
show.targets	0.000	0.000	0.001
summarize	0.026	0.006	0.033
total.library.size.normalization	0.010	0.004	0.015
trim.size.normalization	0.009	0.003	0.013
two.sample.log.ratio	0	0	0
two.sample.permutation.test	0.075	0.011	0.085
venndiagram	0.000	0.000	0.001