Back to Multiple platform build/check report for BioC 3.16: simplified long |
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This page was generated on 2023-04-12 11:05:04 -0400 (Wed, 12 Apr 2023).
Hostname | OS | Arch (*) | R version | Installed pkgs |
---|---|---|---|---|
nebbiolo2 | Linux (Ubuntu 20.04.5 LTS) | x86_64 | 4.2.3 (2023-03-15) -- "Shortstop Beagle" | 4502 |
palomino4 | Windows Server 2022 Datacenter | x64 | 4.2.3 (2023-03-15 ucrt) -- "Shortstop Beagle" | 4282 |
lconway | macOS 12.5.1 Monterey | x86_64 | 4.2.3 (2023-03-15) -- "Shortstop Beagle" | 4310 |
Click on any hostname to see more info about the system (e.g. compilers) (*) as reported by 'uname -p', except on Windows and Mac OS X |
To the developers/maintainers of the fCI package: - Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/fCI.git to reflect on this report. See How and When does the builder pull? When will my changes propagate? for more information. - Make sure to use the following settings in order to reproduce any error or warning you see on this page. |
Package 665/2183 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
fCI 1.28.0 (landing page) Shaojun Tang
| nebbiolo2 | Linux (Ubuntu 20.04.5 LTS) / x86_64 | OK | OK | OK | ![]() | ||||||||
palomino4 | Windows Server 2022 Datacenter / x64 | OK | OK | OK | OK | ![]() | ||||||||
lconway | macOS 12.5.1 Monterey / x86_64 | OK | OK | OK | OK | ![]() | ||||||||
Package: fCI |
Version: 1.28.0 |
Command: /home/biocbuild/bbs-3.16-bioc/R/bin/R CMD check --install=check:fCI.install-out.txt --library=/home/biocbuild/bbs-3.16-bioc/R/site-library --timings fCI_1.28.0.tar.gz |
StartedAt: 2023-04-10 20:40:28 -0400 (Mon, 10 Apr 2023) |
EndedAt: 2023-04-10 20:41:30 -0400 (Mon, 10 Apr 2023) |
EllapsedTime: 62.3 seconds |
RetCode: 0 |
Status: OK |
CheckDir: fCI.Rcheck |
Warnings: 0 |
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.16-bioc/R/bin/R CMD check --install=check:fCI.install-out.txt --library=/home/biocbuild/bbs-3.16-bioc/R/site-library --timings fCI_1.28.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/home/biocbuild/bbs-3.16-bioc/meat/fCI.Rcheck’ * using R version 4.2.3 (2023-03-15) * using platform: x86_64-pc-linux-gnu (64-bit) * using session charset: UTF-8 * checking for file ‘fCI/DESCRIPTION’ ... OK * checking extension type ... Package * this is package ‘fCI’ version ‘1.28.0’ * 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 loading without being on the library search path ... 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 ... ‘fCI.Rmd’... OK NONE * checking re-building of vignette outputs ... OK * checking PDF version of manual ... OK * DONE Status: 3 NOTEs See ‘/home/biocbuild/bbs-3.16-bioc/meat/fCI.Rcheck/00check.log’ for details.
fCI.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.16-bioc/R/bin/R CMD INSTALL fCI ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/bbs-3.16-bioc/R/site-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 ** 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)
fCI.Rcheck/fCI-Ex.timings
name | user | system | elapsed | |
NPCI-class | 0.001 | 0.001 | 0.001 | |
call.npci | 0 | 0 | 0 | |
compute | 0.001 | 0.000 | 0.000 | |
deg.pairwise.fold.change | 0 | 0 | 0 | |
deg.up.down.info | 0 | 0 | 0 | |
deseq.median.ratio.normalization | 0.005 | 0.000 | 0.005 | |
divergence.multivariate.distributions | 0.002 | 0.003 | 0.005 | |
fCI-class | 0.000 | 0.001 | 0.001 | |
fCI.call.by.index | 1.525 | 0.095 | 1.622 | |
figures | 0 | 0 | 0 | |
find.fci.targets | 3.669 | 0.041 | 3.709 | |
find.mid.point | 0.228 | 0.000 | 0.227 | |
get.fold.large.step | 0 | 0 | 0 | |
get.npci.data | 0.001 | 0.000 | 0.001 | |
get.npci.distance.matrix | 0.028 | 0.000 | 0.028 | |
get.outline.index | 0.004 | 0.000 | 0.005 | |
get.protein.fold.step | 0.001 | 0.000 | 0.001 | |
get.rank.combinations | 0.001 | 0.000 | 0.001 | |
get.rna.fold.step | 0.001 | 0.000 | 0.000 | |
intersect.of.lists | 0 | 0 | 0 | |
is.installed | 0.032 | 0.000 | 0.032 | |
normalization | 0 | 0 | 0 | |
npci.gene.by.pvalues | 0.004 | 0.000 | 0.004 | |
npci.index.reconsidered | 0.122 | 0.000 | 0.122 | |
npci.index.to.be.removed | 0 | 0 | 0 | |
npci.venn.diagram | 0.129 | 0.011 | 0.141 | |
pairwise.change.occupancy | 0 | 0 | 0 | |
populate | 0 | 0 | 0 | |
report.target.summary | 0 | 0 | 0 | |
setfCI | 0 | 0 | 0 | |
show.targets | 0.000 | 0.000 | 0.001 | |
summarize | 0.004 | 0.000 | 0.004 | |
total.library.size.normalization | 0.003 | 0.000 | 0.003 | |
trim.size.normalization | 0.003 | 0.000 | 0.003 | |
two.sample.log.ratio | 0 | 0 | 0 | |
two.sample.permutation.test | 0.038 | 0.000 | 0.038 | |
venndiagram | 0 | 0 | 0 | |