revdep/notes.md

In HenrikBengtsson/matrixStats: Functions that Apply to Rows and Columns of Matrices (and to Vectors)

Notes

Setup

> options(Ncpus = 6L)
> install.packages("remotes")
> remotes::install_github("r-lib/revdepcheck")

## Used by R itself
$ revdep/run.R --preinstall RCurl XML

Pre-installation

In order to run these checks successfully on a machine without internet access, make sure to first populate the 'crancache' cache by pre-installing all packages to be tested plus a few more.

## Needed by some packages to be tested (identified by trial and error)
$ revdep/run.R --preinstall Rsamtools sf

## Update current crancache
$ revdep/run.R --preinstall-update

## OpenMx needed by semtree (gcc >= 4.9.3)
$ scl enable devtoolset-6 "revdep/run.R --preinstall OpenMx"

## Rfast needed by IMIFA and obfuscatoR (gcc 6.3.1)
## (https://github.com/RfastOfficial/Rfast/issues/8#issuecomment-586522490)
$ scl enable devtoolset-6 "revdep/run.R --preinstall Rfast"

## RccpAlgos needed by ImpactEffectsize (gcc 5.3.1)
## (https://github.com/jwood000/RcppAlgos/issues/10)
$ scl enable devtoolset-4 "revdep/run.R --preinstall RcppAlgos"

## All packages to be tested
$ revdep/run.R --preinstall-children

Testing

Package with spurious port errors

• DMCFB

Packages that timed out (> 30-minute walltime)

Packages that gave "R CMD check timed out":

• eGST
• flowSpy
• graper
• Luminescence
• MethylAid

Other timeouts:

• maEndToEnd
• metrix
• splatter

Packages that depend on oligo

Packages that depend on oligo, which triggers a _R_CHECK_LENGTH_1_LOGIC2 bug in the methods package when testing on R (<= 3.6.2):

• oligo
• ArrayExpress
• maEndToEnd
• pd.hugene.1.0.st.v1

Manually pre-installing these might help.

Package that requires Internet

The following packages will fail when tested in 'offline' mode because their examples or tests require a working internet connection:

• bumphunter: "cannot open URL 'ftp://ftp.ebi.ac.uk/pub/databases/gencode/Gencode_human/release_25/gencode.v25.annotation.gtf.gz'"
• crossmeta: "AnnotatingURL 'https://bioconductor.org/config.yaml': status was 'Couldn't resolve host, ..."
• DeepBlueR: "Could not resolve host: deepblue.mpi-inf.mpg.de; Name or service not known"
• Doscheda: "Could not resolve host: www.humanmine.org; Name or service not known"
• GAPGOM: "trying to add rname 'http://fantom.gsc.riken.jp/5/datafiles/latest/extra/CAGE_peaks/mm9.cage_peak_phase1and2combined_tpm_ann.osc.txt.gz' produced error: attempt to write a readonly database. Error in bfcrpath(bfc, url) : not all 'rnames' found or unique."
• Pigengene: "Could not resolve host: useast.ensembl.org; Name or service not known"
• PrecisionTrialDrawer: "Could not resolve host: www.cbioportal.org; Name or service not known"
• stm: "cannot open the connection to 'http://goo.gl/VPdxlS'"
• STROMA4: "trying to use CRAN without setting a mirror"
• yarn: "Could not resolve host: www.ensembl.org; Name or service not known"

The following packages produce errors on "No internet connection using 'localHub=TRUE'":

• AMARETTO
• biscuiteer
• DEqMS
• hipathia
• MEAL
• RNAmodR
• sesame

To check these on a machine with internet access, do:

$ revdep/run.R --add bumphunter crossmeta DeepBlueR Doscheda GAPGOM Pigengene PrecisionTrialDrawer stm STROMA4 yarn AMARETTO biscuiteer DEqMS hipathia MEAL RNAmodR sesame
$ NSLOTS=8 revdep/run.R

Missing dependencies

• CATALYST: "Error in loadNamespace(name) : there is no package called ‘uwot’"
• muscat: "statmod package required but is not installed"

Package with R_CHECK_LENGTH_1_*_ errors

• SIAMCAT: "Error in pred.names != "" && !is.null(pred.names) : 'length(x) = 2 > 1' in coercion to 'logical(1)'"

• https://bioconductor.org/checkResults/devel/bioc-LATEST/SIAMCAT/malbec2-checksrc.html

• VanillaICE: "Error in msg && (requiredAssays() %in% names(assays(object))) : 'length(x) = 2 > 1' in coercion to 'logical(1)'"

• https://bioconductor.org/checkResults/devel/bioc-LATEST/VanillaICE/malbec2-checksrc.html

Packages with installation errors (?!?)

• SICtools: "bam_tview_curses.c:5:20: fatal error: curses.h: No such file or directory"

HenrikBengtsson/matrixStats documentation built on April 12, 2024, 5:32 a.m.