Package: fCI

Version: 1.13.0

Command: /home/biocbuild/bbs-3.9-bioc/R/bin/R CMD check --install=check:fCI.install-out.txt --library=/home/biocbuild/bbs-3.9-bioc/R/library --no-vignettes --timings fCI_1.13.0.tar.gz

StartedAt: 2019-04-09 00:27:52 -0400 (Tue, 09 Apr 2019)

EndedAt: 2019-04-09 00:28:36 -0400 (Tue, 09 Apr 2019)

EllapsedTime: 43.5 seconds

RetCode: 0

Status:  OK

CheckDir: fCI.Rcheck

Warnings: 0

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### Running command:
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###   /home/biocbuild/bbs-3.9-bioc/R/bin/R CMD check --install=check:fCI.install-out.txt --library=/home/biocbuild/bbs-3.9-bioc/R/library --no-vignettes --timings fCI_1.13.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.9-bioc/meat/fCI.Rcheck’
* using R Under development (unstable) (2019-03-18 r76245)
* using platform: x86_64-pc-linux-gnu (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 ‘1.13.0’
* 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 ... OK
* 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: 3 NOTEs
See
  ‘/home/biocbuild/bbs-3.9-bioc/meat/fCI.Rcheck/00check.log’
for details.

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### Running command:
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###   /home/biocbuild/bbs-3.9-bioc/R/bin/R CMD INSTALL fCI
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* installing to library ‘/home/biocbuild/bbs-3.9-bioc/R/library’
* installing *source* package ‘fCI’ ...
** using staged installation
** R
** data
** inst
** byte-compile and prepare package for lazy loading
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
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (fCI)

name	user	system	elapsed
NPCI-class	0.003	0.000	0.003
call.npci	0.000	0.000	0.001
compute	0.000	0.000	0.001
deg.pairwise.fold.change	0.001	0.000	0.000
deg.up.down.info	0	0	0
deseq.median.ratio.normalization	0.007	0.004	0.011
divergence.multivariate.distributions	0.01	0.00	0.01
fCI-class	0.001	0.000	0.002
fCI.call.by.index	2.043	0.111	2.156
figures	0	0	0
find.fci.targets	4.704	0.039	4.758
find.mid.point	0.299	0.000	0.299
get.fold.large.step	0	0	0
get.npci.data	0.001	0.000	0.002
get.npci.distance.matrix	0.02	0.00	0.02
get.outline.index	0.004	0.000	0.004
get.protein.fold.step	0.000	0.000	0.001
get.rank.combinations	0.001	0.000	0.001
get.rna.fold.step	0	0	0
intersect.of.lists	0.000	0.001	0.000
is.installed	0.023	0.003	0.025
normalization	0	0	0
npci.gene.by.pvalues	0.004	0.000	0.004
npci.index.reconsidered	0.11	0.00	0.11
npci.index.to.be.removed	0	0	0
npci.venn.diagram	0.163	0.004	0.175
pairwise.change.occupancy	0.000	0.001	0.000
populate	0	0	0
report.target.summary	0	0	0
setfCI	0.000	0.001	0.001
show.targets	0	0	0
summarize	0.004	0.000	0.004
total.library.size.normalization	0.000	0.003	0.004
trim.size.normalization	0.004	0.000	0.004
two.sample.log.ratio	0.000	0.000	0.001
two.sample.permutation.test	0.032	0.000	0.031
venndiagram	0	0	0