Mariano J Alvarez
| Snapshot Date: 2022-03-17 13:55:23 -0400 (Thu, 17 Mar 2022) |
| git_url: https://git.bioconductor.org/packages/diggit |
| git_branch: master |
| git_last_commit: a76959f |
| git_last_commit_date: 2021-10-26 12:19:08 -0400 (Tue, 26 Oct 2021) |
| Back to Multiple platform build/check report for BioC 3.15 |
|
This page was generated on 2022-03-18 11:07:23 -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 diggit package: - Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/diggit.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 518/2090 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| diggit 1.27.0 (landing page) Mariano J Alvarez
| nebbiolo1 | Linux (Ubuntu 20.04.4 LTS) / x86_64 | OK | OK | WARNINGS | | ||||||||
| riesling1 | Windows Server 2019 Standard / x64 | OK | OK | WARNINGS | OK | |||||||||
| palomino3 | Windows Server 2022 Datacenter / x64 | OK | OK | WARNINGS | OK | | ||||||||
| merida1 | macOS 10.14.6 Mojave / x86_64 | OK | OK | WARNINGS | OK | | ||||||||
| Package: diggit |
| Version: 1.27.0 |
| Command: D:\biocbuild\bbs-3.15-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:diggit.install-out.txt --library=D:\biocbuild\bbs-3.15-bioc\R\library --no-vignettes --timings diggit_1.27.0.tar.gz |
| StartedAt: 2022-03-17 18:56:44 -0400 (Thu, 17 Mar 2022) |
| EndedAt: 2022-03-17 19:00:43 -0400 (Thu, 17 Mar 2022) |
| EllapsedTime: 239.5 seconds |
| RetCode: 0 |
| Status: WARNINGS |
| CheckDir: diggit.Rcheck |
| Warnings: 3 |
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### Running command:
###
### D:\biocbuild\bbs-3.15-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:diggit.install-out.txt --library=D:\biocbuild\bbs-3.15-bioc\R\library --no-vignettes --timings diggit_1.27.0.tar.gz
###
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* using log directory 'D:/biocbuild/bbs-3.15-bioc/meat/diggit.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 'diggit/DESCRIPTION' ... OK
* this is package 'diggit' version '1.27.0'
* checking package namespace information ... OK
* checking package dependencies ... OK
* 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 'diggit' can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking 'build' directory ... OK
* checking DESCRIPTION meta-information ... NOTE
Malformed Description field: should contain one or more complete sentences.
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... WARNING
Invalid citation information in 'inst/CITATION':
Error in citeEntry(entry = "article", author = c(person(c("Mariano", "J"), "Alvarez"), person(c("James", "C"), "Chen"), person("Andrea", "Califano")), title = "{DIGGIT}: a Bioconductor package to infer genetic variants driving cellular phenotypes", journal = "Bioinformatics", year = 2015, volume = 31, number = 24, pages = "4032--4", textVersion = "Alvarez, M.J., Chen, J.C., and Califano, A. (2015) DIGGIT: a Bioconductor package to infer genetic variants driving cellular phenotypes. Bioinformatics 31(24):4032--4."): could not find function "citeEntry"
* 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 ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
aecdf: no visible global function definition for 'quantile'
aecdf: no visible global function definition for 'ecdf'
aecdf: no visible global function definition for 'knots'
aecdf: no visible global function definition for 'lm'
aecdf: no visible global function definition for 'approxfun'
aecdf : dnull: no visible global function definition for 'predict'
aecdf : dnull: no visible global function definition for 'qnorm'
conditionalInternal: no visible global function definition for
'p.adjust'
conditionalInternal : <anonymous>: no visible global function
definition for 'fisher.test'
conditionalInternal: no visible global function definition for 'hclust'
conditionalInternal: no visible global function definition for
'as.dist'
conditionalInternal: no visible global function definition for 'cutree'
conditionalInternal : <anonymous> : <anonymous> : <anonymous>: no
visible global function definition for 'fisher.test'
conditionalInternal : <anonymous> : <anonymous>: no visible global
function definition for 'fisher.test'
correlation : <anonymous>: no visible global function definition for
'cor'
correlation: no visible global function definition for 'cor'
cortest: no visible global function definition for 'pnorm'
distMode: no visible global function definition for 'density'
fet: no visible global function definition for 'fisher.test'
internalMIfb: no visible global function definition for 'dnorm'
mutualInfo: no visible global function definition for 'qnorm'
mutualInfo: no visible global function definition for 'combn'
mutualInfo: no visible global function definition for 'txtProgressBar'
mutualInfo : <anonymous>: no visible global function definition for
'setTxtProgressBar'
plothm: no visible global function definition for 'rgb2hsv'
plothm: no visible global function definition for 'col2rgb'
plothm: no visible global function definition for 'hsv'
plothm: no visible global function definition for 'image'
plothm: no visible global function definition for 'box'
aqtl,diggit: no visible global function definition for 'p.adjust'
aqtl,diggit: no visible global function definition for 'pnorm'
conditional,diggit: no visible global function definition for
'p.adjust'
conditional,diggit: no visible global function definition for 'pnorm'
conditional,diggit: no visible global function definition for
'txtProgressBar'
conditional,diggit : <anonymous>: no visible global function definition
for 'setTxtProgressBar'
marina,matrix: no visible global function definition for 'qnorm'
mindyFiltering,diggit: no visible global function definition for
'p.adjust'
plot,diggit-ANY: no visible global function definition for 'abline'
plot,diggit-ANY: no visible global function definition for 'text'
plot,diggit-ANY: no visible global function definition for 'axis'
Undefined global functions or variables:
abline approxfun as.dist axis box col2rgb combn cor cutree density
dnorm ecdf fisher.test hclust hsv image knots lm p.adjust pnorm
predict qnorm quantile rgb2hsv setTxtProgressBar text txtProgressBar
Consider adding
importFrom("grDevices", "col2rgb", "hsv", "rgb2hsv")
importFrom("graphics", "abline", "axis", "box", "image", "text")
importFrom("stats", "approxfun", "as.dist", "cor", "cutree", "density",
"dnorm", "ecdf", "fisher.test", "hclust", "knots", "lm",
"p.adjust", "pnorm", "predict", "qnorm", "quantile")
importFrom("utils", "combn", "setTxtProgressBar", "txtProgressBar")
to your NAMESPACE file.
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... WARNING
Undocumented S4 methods:
generic 'plot' and siglist 'diggit,ANY'
All user-level objects in a package (including S4 classes and methods)
should have documentation entries.
See chapter 'Writing R documentation files' in the 'Writing R
Extensions' manual.
* checking for code/documentation mismatches ... WARNING
Codoc mismatches from documentation object 'aecdf':
aecdf
Code: function(dnull, symmetric = FALSE, n = 100)
Docs: function(dnull, symmetric = FALSE)
Argument names in code not in docs:
n
* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking files in 'vignettes' ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
user system elapsed
marina-methods 69.98 46.41 116.41
aqtl-methods 12.42 3.79 16.22
conditional-methods 12.78 1.83 14.61
diggit-plot 12.11 0.95 13.06
* 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 WARNINGs, 2 NOTEs
See
'D:/biocbuild/bbs-3.15-bioc/meat/diggit.Rcheck/00check.log'
for details.
diggit.Rcheck/00install.out
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### Running command:
###
### D:\biocbuild\bbs-3.15-bioc\R\bin\R.exe CMD INSTALL diggit
###
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* installing to library 'D:/biocbuild/bbs-3.15-bioc/R/library'
* installing *source* package 'diggit' ...
** using staged installation
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
converting help for package 'diggit'
finding HTML links ... done
aecdf html
aqtl-methods html
conditional-methods html
correlation html
diggit-class html
diggit-methods html
diggit-plot html
fcnv-methods html
marina-methods html
mutualInfo 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 (diggit)
Making 'packages.html' ...Warning in packageDescription(i, lib.loc = lib, fields = "Title", encoding = "UTF-8") :
DESCRIPTION file of package 'gsean' is missing or broken
done
diggit.Rcheck/diggit-Ex.timings
| name | user | system | elapsed | |
| aqtl-methods | 12.42 | 3.79 | 16.22 | |
| conditional-methods | 12.78 | 1.83 | 14.61 | |
| correlation | 0 | 0 | 0 | |
| diggit-class | 1.33 | 0.04 | 1.37 | |
| diggit-methods | 3.86 | 0.24 | 4.10 | |
| diggit-plot | 12.11 | 0.95 | 13.06 | |
| fcnv-methods | 1.80 | 0.22 | 2.01 | |
| marina-methods | 69.98 | 46.41 | 116.41 | |
| mutualInfo | 1.78 | 0.01 | 1.80 | |