Shaojun Tang
| Snapshot Date: 2019-04-15 17:01:12 -0400 (Mon, 15 Apr 2019) |
| URL: https://git.bioconductor.org/packages/fCI |
| Branch: RELEASE_3_8 |
| Last Commit: 1d158e8 |
| Last Changed Date: 2018-10-30 11:41:58 -0400 (Tue, 30 Oct 2018) |
| Back to Multiple platform build/check report for BioC 3.8 |
|
This page was generated on 2019-04-16 11:51:26 -0400 (Tue, 16 Apr 2019).
| Package 511/1649 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
| fCI 1.12.0 Shaojun Tang
| malbec1 | Linux (Ubuntu 16.04.6 LTS) / x86_64 | OK | OK | [ OK ] | | ||||||
| merida1 | OS X 10.11.6 El Capitan / x86_64 | OK | OK | WARNINGS | OK | |
| Package: fCI |
| Version: 1.12.0 |
| Command: /home/biocbuild/bbs-3.8-bioc/R/bin/R CMD check --install=check:fCI.install-out.txt --library=/home/biocbuild/bbs-3.8-bioc/R/library --no-vignettes --timings fCI_1.12.0.tar.gz |
| StartedAt: 2019-04-15 23:53:54 -0400 (Mon, 15 Apr 2019) |
| EndedAt: 2019-04-15 23:54:33 -0400 (Mon, 15 Apr 2019) |
| EllapsedTime: 39.6 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: fCI.Rcheck |
| Warnings: 0 |
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### Running command:
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### /home/biocbuild/bbs-3.8-bioc/R/bin/R CMD check --install=check:fCI.install-out.txt --library=/home/biocbuild/bbs-3.8-bioc/R/library --no-vignettes --timings fCI_1.12.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.8-bioc/meat/fCI.Rcheck’
* using R version 3.5.3 (2019-03-11)
* 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 ‘1.12.0’
* 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-3.8-bioc/meat/fCI.Rcheck/00check.log’
for details.
fCI.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.8-bioc/R/bin/R CMD INSTALL fCI ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/bbs-3.8-bioc/R/library’ * installing *source* package ‘fCI’ ... ** 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 * DONE (fCI)
fCI.Rcheck/fCI-Ex.timings
| name | user | system | elapsed | |
| NPCI-class | 0.000 | 0.000 | 0.003 | |
| call.npci | 0 | 0 | 0 | |
| compute | 0 | 0 | 0 | |
| deg.pairwise.fold.change | 0.000 | 0.000 | 0.001 | |
| deg.up.down.info | 0 | 0 | 0 | |
| deseq.median.ratio.normalization | 0.012 | 0.000 | 0.012 | |
| divergence.multivariate.distributions | 0.012 | 0.000 | 0.010 | |
| fCI-class | 0.000 | 0.000 | 0.002 | |
| fCI.call.by.index | 1.920 | 0.132 | 2.068 | |
| figures | 0 | 0 | 0 | |
| find.fci.targets | 3.940 | 0.004 | 3.950 | |
| find.mid.point | 0.528 | 0.000 | 0.527 | |
| get.fold.large.step | 0 | 0 | 0 | |
| get.npci.data | 0.000 | 0.004 | 0.002 | |
| get.npci.distance.matrix | 0.04 | 0.00 | 0.04 | |
| get.outline.index | 0.024 | 0.000 | 0.023 | |
| get.protein.fold.step | 0.000 | 0.000 | 0.001 | |
| get.rank.combinations | 0.000 | 0.000 | 0.001 | |
| get.rna.fold.step | 0 | 0 | 0 | |
| intersect.of.lists | 0 | 0 | 0 | |
| is.installed | 0.036 | 0.004 | 0.041 | |
| normalization | 0 | 0 | 0 | |
| npci.gene.by.pvalues | 0.008 | 0.000 | 0.008 | |
| npci.index.reconsidered | 0.168 | 0.004 | 0.171 | |
| npci.index.to.be.removed | 0 | 0 | 0 | |
| npci.venn.diagram | 0.260 | 0.016 | 0.276 | |
| pairwise.change.occupancy | 0.000 | 0.000 | 0.001 | |
| populate | 0 | 0 | 0 | |
| report.target.summary | 0 | 0 | 0 | |
| setfCI | 0.000 | 0.000 | 0.001 | |
| show.targets | 0.000 | 0.000 | 0.001 | |
| summarize | 0.008 | 0.000 | 0.009 | |
| total.library.size.normalization | 0.008 | 0.000 | 0.006 | |
| trim.size.normalization | 0.008 | 0.000 | 0.007 | |
| two.sample.log.ratio | 0 | 0 | 0 | |
| two.sample.permutation.test | 0.04 | 0.00 | 0.04 | |
| venndiagram | 0 | 0 | 0 | |