Shaojun Tang
| Snapshot Date: 2022-03-17 13:55:23 -0400 (Thu, 17 Mar 2022) |
| git_url: https://git.bioconductor.org/packages/fCI |
| git_branch: master |
| git_last_commit: 76cc2d1 |
| git_last_commit_date: 2021-10-26 12:21:13 -0400 (Tue, 26 Oct 2021) |
| Back to Multiple platform build/check report for BioC 3.15 |
|
This page was generated on 2022-03-18 11:07:29 -0400 (Fri, 18 Mar 2022).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo1 | Linux (Ubuntu 20.04.4 LTS) | x86_64 | R Under development (unstable) (2022-02-17 r81757) -- "Unsuffered Consequences" | 4334 |
| riesling1 | Windows Server 2019 Standard | x64 | R Under development (unstable) (2021-11-21 r81221) -- "Unsuffered Consequences" | 4097 |
| palomino3 | Windows Server 2022 Datacenter | x64 | R Under development (unstable) (2022-02-17 r81757 ucrt) -- "Unsuffered Consequences" | 4083 |
| merida1 | macOS 10.14.6 Mojave | x86_64 | R Under development (unstable) (2022-03-02 r81842) -- "Unsuffered Consequences" | 4134 |
| 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? here for more information. - Make sure to use the following settings in order to reproduce any error or warning you see on this page. |
| Package 633/2090 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| fCI 1.25.0 (landing page) Shaojun Tang
| nebbiolo1 | Linux (Ubuntu 20.04.4 LTS) / x86_64 | OK | OK | OK | | ||||||||
| riesling1 | Windows Server 2019 Standard / x64 | OK | OK | OK | OK | |||||||||
| palomino3 | Windows Server 2022 Datacenter / x64 | OK | OK | OK | OK | | ||||||||
| merida1 | macOS 10.14.6 Mojave / x86_64 | OK | OK | OK | OK | | ||||||||
| Package: fCI |
| Version: 1.25.0 |
| Command: D:\biocbuild\bbs-3.15-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:fCI.install-out.txt --library=D:\biocbuild\bbs-3.15-bioc\R\library --no-vignettes --timings fCI_1.25.0.tar.gz |
| StartedAt: 2022-03-17 19:04:55 -0400 (Thu, 17 Mar 2022) |
| EndedAt: 2022-03-17 19:05:45 -0400 (Thu, 17 Mar 2022) |
| EllapsedTime: 50.4 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: fCI.Rcheck |
| Warnings: 0 |
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### Running command:
###
### D:\biocbuild\bbs-3.15-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:fCI.install-out.txt --library=D:\biocbuild\bbs-3.15-bioc\R\library --no-vignettes --timings fCI_1.25.0.tar.gz
###
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* using log directory 'D:/biocbuild/bbs-3.15-bioc/meat/fCI.Rcheck'
* using R Under development (unstable) (2021-11-21 r81221)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'fCI/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'fCI' version '1.25.0'
* 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 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
'D:/biocbuild/bbs-3.15-bioc/meat/fCI.Rcheck/00check.log'
for details.
fCI.Rcheck/00install.out
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###
### Running command:
###
### D:\biocbuild\bbs-3.15-bioc\R\bin\R.exe CMD INSTALL fCI
###
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* installing to library 'D:/biocbuild/bbs-3.15-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
converting help for package 'fCI'
finding HTML links ... done
NPCI-class html
call.npci-methods html
call.npci html
compute-methods html
compute html
deg.pairwise.fold.change html
deg.up.down.info html
deseq.median.ratio.normalization html
divergence.multivariate.distributions html
fCI-class html
fCI.call.by.index html
fci.data html
figures-methods html
figures html
find.fci.targets-methods html
find.fci.targets html
find.mid.point html
get.fold.large.step html
get.npci.data html
get.npci.distance.matrix html
get.outline.index html
get.protein.fold.step html
get.rank.combinations html
get.rna.fold.step html
initialize-methods html
intersect.of.lists html
is.installed html
multi.dimensional.fci.data html
normalization-methods html
normalization html
npci.gene.by.pvalues html
npci.index.reconsidered html
npci.index.to.be.removed html
npci.venn.diagram html
pairwise.change.occupancy html
populate-methods html
populate html
report.target.summary html
setfCI-methods html
setfCI html
show.targets-methods html
show.targets html
summarize-methods html
summarize html
total.library.size.normalization html
trim.size.normalization html
two.sample.log.ratio html
two.sample.permutation.test html
venndiagram-methods html
venndiagram html
** 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)
Making 'packages.html' ... done
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 | 0 | 0 | |
| deg.up.down.info | 0 | 0 | 0 | |
| deseq.median.ratio.normalization | 0 | 0 | 0 | |
| divergence.multivariate.distributions | 0 | 0 | 0 | |
| fCI-class | 0 | 0 | 0 | |
| fCI.call.by.index | 1.52 | 0.74 | 2.25 | |
| figures | 0 | 0 | 0 | |
| find.fci.targets | 2.83 | 0.29 | 3.12 | |
| find.mid.point | 0.19 | 0.05 | 0.24 | |
| get.fold.large.step | 0.01 | 0.00 | 0.01 | |
| get.npci.data | 0 | 0 | 0 | |
| get.npci.distance.matrix | 0.02 | 0.00 | 0.02 | |
| get.outline.index | 0 | 0 | 0 | |
| get.protein.fold.step | 0 | 0 | 0 | |
| get.rank.combinations | 0 | 0 | 0 | |
| get.rna.fold.step | 0 | 0 | 0 | |
| intersect.of.lists | 0 | 0 | 0 | |
| is.installed | 0.03 | 0.00 | 0.03 | |
| normalization | 0 | 0 | 0 | |
| npci.gene.by.pvalues | 0 | 0 | 0 | |
| npci.index.reconsidered | 0.11 | 0.00 | 0.11 | |
| npci.index.to.be.removed | 0 | 0 | 0 | |
| npci.venn.diagram | 0.08 | 0.03 | 0.13 | |
| 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 | 0.00 | 0.02 | 0.01 | |
| two.sample.log.ratio | 0 | 0 | 0 | |
| two.sample.permutation.test | 0.01 | 0.00 | 0.02 | |
| venndiagram | 0 | 0 | 0 | |