Back to Multiple platform build/check report for BioC 3.20: simplified long |
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This page was generated on 2024-08-21 11:41 -0400 (Wed, 21 Aug 2024).
Hostname | OS | Arch (*) | R version | Installed pkgs |
---|---|---|---|---|
nebbiolo2 | Linux (Ubuntu 22.04.3 LTS) | x86_64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4703 |
palomino8 | Windows Server 2022 Datacenter | x64 | 4.4.1 (2024-06-14 ucrt) -- "Race for Your Life" | 4440 |
lconway | macOS 12.7.1 Monterey | x86_64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4472 |
kjohnson3 | macOS 13.6.5 Ventura | arm64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4421 |
kunpeng2 | Linux (openEuler 22.03 LTS-SP1) | aarch64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4414 |
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 |
Package 692/2255 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
fCI 1.35.0 (landing page) Shaojun Tang
| nebbiolo2 | Linux (Ubuntu 22.04.3 LTS) / x86_64 | OK | OK | OK | ![]() | ||||||||
palomino8 | Windows Server 2022 Datacenter / x64 | OK | OK | OK | OK | ![]() | ||||||||
lconway | macOS 12.7.1 Monterey / x86_64 | OK | OK | OK | OK | ![]() | ||||||||
kjohnson3 | macOS 13.6.5 Ventura / arm64 | OK | OK | OK | OK | ![]() | ||||||||
kunpeng2 | Linux (openEuler 22.03 LTS-SP1) / aarch64 | OK | OK | OK | ||||||||||
To the developers/maintainers of the fCI package: - 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 Troubleshooting Build Report for more information. - Use the following Renviron settings to reproduce errors and warnings. - If 'R CMD check' started to fail recently on the Linux builder(s) over a missing dependency, add the missing dependency to 'Suggests:' in your DESCRIPTION file. See Renviron.bioc for more information. |
Package: fCI |
Version: 1.35.0 |
Command: F:\biocbuild\bbs-3.20-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:fCI.install-out.txt --library=F:\biocbuild\bbs-3.20-bioc\R\library --no-vignettes --timings fCI_1.35.0.tar.gz |
StartedAt: 2024-08-21 00:45:29 -0400 (Wed, 21 Aug 2024) |
EndedAt: 2024-08-21 00:46:42 -0400 (Wed, 21 Aug 2024) |
EllapsedTime: 72.2 seconds |
RetCode: 0 |
Status: OK |
CheckDir: fCI.Rcheck |
Warnings: 0 |
############################################################################## ############################################################################## ### ### Running command: ### ### F:\biocbuild\bbs-3.20-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:fCI.install-out.txt --library=F:\biocbuild\bbs-3.20-bioc\R\library --no-vignettes --timings fCI_1.35.0.tar.gz ### ############################################################################## ############################################################################## * using log directory 'F:/biocbuild/bbs-3.20-bioc/meat/fCI.Rcheck' * using R version 4.4.1 (2024-06-14 ucrt) * using platform: x86_64-w64-mingw32 * R was compiled by gcc.exe (GCC) 13.2.0 GNU Fortran (GCC) 13.2.0 * running under: Windows Server 2022 x64 (build 20348) * using session charset: UTF-8 * using option '--no-vignettes' * checking for file 'fCI/DESCRIPTION' ... OK * checking extension type ... Package * this is package 'fCI' version '1.35.0' * checking package namespace information ... NOTE Found export directives that require package 'methods': 'exportClasses' 'exportMethods' Remove all such namespace directives (if obsolete) or ensure that the DESCRIPTION Depends or Imports field contains 'methods'. * 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 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 code 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 ... NOTE Argument items with no description in Rd file 'compute.Rd': '.Object' Argument items with no description in Rd file 'figures.Rd': '.Object' Argument items with no description in Rd file 'find.mid.point.Rd': 'Y' Argument items with no description in Rd file 'get.npci.data.Rd': 'sample.data.normalized' 'wt.index' 'df.index' Argument items with no description in Rd file 'get.npci.distance.matrix.Rd': 'npci.data' 'null.data.start' 'diff.data.start' 'choice' 'rank.index.to.be.removed' 'expr.by.fold' 'ctr.indexes' 'trt.indexes' 'use.intersect' 'symmetric.fold' 'fold.cutoff.list' Argument items with no description in Rd file 'get.outline.index.Rd': 'values' Argument items with no description in Rd file 'populate.Rd': '.Object' * 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 Examples with CPU (user + system) or elapsed time > 5s user system elapsed find.fci.targets 5.31 0.34 5.67 fCI.call.by.index 2.53 2.03 5.09 * checking for unstated dependencies in vignettes ... OK * checking package vignettes ... 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 'F:/biocbuild/bbs-3.20-bioc/meat/fCI.Rcheck/00check.log' for details.
fCI.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### F:\biocbuild\bbs-3.20-bioc\R\bin\R.exe CMD INSTALL fCI ### ############################################################################## ############################################################################## * installing to library 'F:/biocbuild/bbs-3.20-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 ** 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 | 0 | 0 | |
call.npci | 0 | 0 | 0 | |
compute | 0 | 0 | 0 | |
deg.pairwise.fold.change | 0.01 | 0.00 | 0.02 | |
deg.up.down.info | 0 | 0 | 0 | |
deseq.median.ratio.normalization | 0 | 0 | 0 | |
divergence.multivariate.distributions | 0.02 | 0.00 | 0.01 | |
fCI-class | 0 | 0 | 0 | |
fCI.call.by.index | 2.53 | 2.03 | 5.09 | |
figures | 0 | 0 | 0 | |
find.fci.targets | 5.31 | 0.34 | 5.67 | |
find.mid.point | 0.47 | 0.03 | 0.50 | |
get.fold.large.step | 0 | 0 | 0 | |
get.npci.data | 0.02 | 0.00 | 0.02 | |
get.npci.distance.matrix | 0.03 | 0.00 | 0.03 | |
get.outline.index | 0 | 0 | 0 | |
get.protein.fold.step | 0.01 | 0.00 | 0.01 | |
get.rank.combinations | 0 | 0 | 0 | |
get.rna.fold.step | 0 | 0 | 0 | |
intersect.of.lists | 0 | 0 | 0 | |
is.installed | 0.04 | 0.02 | 0.05 | |
normalization | 0 | 0 | 0 | |
npci.gene.by.pvalues | 0 | 0 | 0 | |
npci.index.reconsidered | 0.15 | 0.03 | 0.19 | |
npci.index.to.be.removed | 0 | 0 | 0 | |
npci.venn.diagram | 0.11 | 0.03 | 0.16 | |
pairwise.change.occupancy | 0 | 0 | 0 | |
populate | 0 | 0 | 0 | |
report.target.summary | 0 | 0 | 0 | |
setfCI | 0 | 0 | 0 | |
show.targets | 0 | 0 | 0 | |
summarize | 0 | 0 | 0 | |
total.library.size.normalization | 0 | 0 | 0 | |
trim.size.normalization | 0.01 | 0.00 | 0.02 | |
two.sample.log.ratio | 0 | 0 | 0 | |
two.sample.permutation.test | 0.05 | 0.00 | 0.04 | |
venndiagram | 0 | 0 | 0 | |