Closed kakopo closed 1 year ago
Hi @kakopo
Thanks for submitting your package. We are taking a quick look at it and you will hear back from us soon.
The DESCRIPTION file for this package is:
Package: BSgenomeForge
Title: Forge BSgenome data packages
Description: A set of tools to forge BSgenome data packages. Supersedes the
old seed-based tools from the BSgenome software package. This package
allows the user to create a BSgenome data package in one function call,
simplifying the old seed-based process.
biocViews: Genetics, Infrastructure, DataRepresentation, Annotation,
GenomeAnnotation, Sequencing, Alignment, DataImport,
SequenceMatching
URL: https://bioconductor.org/packages/BSgenomeForge
BugReports: https://github.com/Bioconductor/BSgenomeForge/issues
Version: 0.99.0
License: Artistic-2.0
Encoding: UTF-8
Authors@R: c(
person("Hervé", "Pagès", role=c("aut", "cre"),
email="hpages.on.github@gmail.com"),
person("Atuhurira Kirabo", "Kakopo", role="aut"),
person("Emmanuel Chigozie", "Elendu", role="ctb"),
person("Prisca Chidimma", "Maduka", role="ctb"))
Depends: R (>= 4.3.0), methods, BiocGenerics, S4Vectors, IRanges,
GenomeInfoDb (>= 1.33.17), Biostrings, BSgenome
Imports: utils, stats, Biobase, rtracklayer
Suggests: GenomicRanges, GenomicFeatures, testthat, knitr, rmarkdown,
BiocStyle, devtools
VignetteBuilder: knitr
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Dear Package contributor,
This is the automated single package builder at bioconductor.org.
Your package has been built on Linux, Mac, and Windows.
On one or more platforms, the build results were: "WARNINGS". This may mean there is a problem with the package that you need to fix. Or it may mean that there is a problem with the build system itself.
Please see the build report for more details. This link will be active for 21 days.
Remember: if you submitted your package after July 7th, 2020,
when making changes to your repository push to
git@git.bioconductor.org:packages/BSgenomeForge
to trigger a new build.
A quick tutorial for setting up remotes and pushing to upstream can be found here.
Hi @kakopo,
Thank you for submitting BSgenomeForge to Bioconductor.
Overall, the package is in good shape and close to being ready for acceptance.
In my review below I have separated the issues into Required and Recommended points that I would ask you to address before the package can be accepted. Would you please provide line-by-line comments to my initial review so that I know what changes I'm looking for in my re-review.
Cheers, Pete
README-Oct2022.md
from the git repository."cre"
included as their role
in the Authors@R
field of the DESCRIPTION
(currently it's @hpages)..Rd
files and the vignette should probably set destdir = tempdir()
so as not to pollute the user's or build machine's working directory.suppressPackageStartupMessages(library(BSgenomeForge))
forgeBSgenomeDataPkgFromNCBI(assembly_accession="GCA_009729545.1",
organism="Acidianus infernus",
pkg_maintainer="Jane Doe <janedoe@gmail.com>")
#> Creating package in ./BSgenome.Ainfernus.NCBI.ASM972954v1
#> Warning in file.rename(filepath, to): cannot rename file
#> '/var/folders/xb/3bl_ghcd3l5gcp6lxnkzy81h0000gn/T//RtmpPS7qnp/single_sequences.2bit'
#> to './BSgenome.Ainfernus.NCBI.ASM972954v1/inst/extdata/single_sequences.2bit',
#> reason 'No such file or directory'
R CMD check
and R CMD install
on the BSgenome.Ainfernus.NCBI.ASM972954v1
example created during the vignette both failed (run via command line or with devtools wrappers). Please clarify why this fails and fix if it should be working.suppressPackageStartupMessages(library(BSgenomeForge))
forgeBSgenomeDataPkgFromNCBI(assembly_accession="GCA_009729545.1",
organism="Acidianus infernus",
pkg_maintainer="Jane Doe <janedoe@gmail.com>")
#> Creating package in ./BSgenome.Ainfernus.NCBI.ASM972954v1
#> Warning in file.rename(filepath, to): cannot rename file
#> '/var/folders/xb/3bl_ghcd3l5gcp6lxnkzy81h0000gn/T//RtmpjMSWrA/single_sequences.2bit'
#> to './BSgenome.Ainfernus.NCBI.ASM972954v1/inst/extdata/single_sequences.2bit',
#> reason 'No such file or directory'
devtools::build("./BSgenome.Ainfernus.NCBI.ASM972954v1")
#> ── R CMD build ─────────────────────────────────────────────────────────────────
#> * checking for file ‘/private/var/folders/xb/3bl_ghcd3l5gcp6lxnkzy81h0000gn/T/RtmpFXx1Ut/reprex-173f83094461c-beton-fish/BSgenome.Ainfernus.NCBI.ASM972954v1/DESCRIPTION’ ... OK
#> * preparing ‘BSgenome.Ainfernus.NCBI.ASM972954v1’:
#> * checking DESCRIPTION meta-information ... OK
#> * checking for LF line-endings in source and make files and shell scripts
#> * checking for empty or unneeded directories
#> * building ‘BSgenome.Ainfernus.NCBI.ASM972954v1_1.0.0.tar.gz’
#> [1] "/private/var/folders/xb/3bl_ghcd3l5gcp6lxnkzy81h0000gn/T/RtmpFXx1Ut/reprex-173f83094461c-beton-fish/BSgenome.Ainfernus.NCBI.ASM972954v1_1.0.0.tar.gz"
devtools::check_built("BSgenome.Ainfernus.NCBI.ASM972954v1_1.0.0.tar.gz")
#> ══ Checking ════════════════════════════════════════════════════════════════════
#> Setting env vars:
#> • _R_CHECK_CRAN_INCOMING_REMOTE_ : FALSE
#> • _R_CHECK_CRAN_INCOMING_ : FALSE
#> • _R_CHECK_FORCE_SUGGESTS_ : FALSE
#> • _R_CHECK_PACKAGES_USED_IGNORE_UNUSED_IMPORTS_: FALSE
#> ── R CMD check ─────────────────────────────────────────────────────────────────
#> * using log directory ‘/private/var/folders/xb/3bl_ghcd3l5gcp6lxnkzy81h0000gn/T/RtmpjMSWrA/BSgenome.Ainfernus.NCBI.ASM972954v1.Rcheck’
#> * using R Under development (unstable) (2023-02-13 r83829)
#> * using platform: aarch64-apple-darwin20 (64-bit)
#> * R was compiled by
#> Apple clang version 13.0.0 (clang-1300.0.29.3)
#> GNU Fortran (GCC) 12.0.1 20220312 (experimental)
#> * running under: macOS Ventura 13.2.1
#> * using session charset: UTF-8
#> * using options ‘--no-manual --as-cran’
#> * checking for file ‘BSgenome.Ainfernus.NCBI.ASM972954v1/DESCRIPTION’ ... OK
#> * this is package ‘BSgenome.Ainfernus.NCBI.ASM972954v1’ version ‘1.0.0’
#> * 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 executable files ... OK
#> * checking for hidden files and directories ... OK
#> * checking for portable file names ... OK
#> * checking for sufficient/correct file permissions ... OK
#> * checking whether package ‘BSgenome.Ainfernus.NCBI.ASM972954v1’ can be installed ... ERROR
#> Installation failed.
#> See ‘/private/var/folders/xb/3bl_ghcd3l5gcp6lxnkzy81h0000gn/T/RtmpjMSWrA/BSgenome.Ainfernus.NCBI.ASM972954v1.Rcheck/00install.out’ for details.
#> * DONE
#>
#> Status: 1 ERROR
#> See
#> ‘/private/var/folders/xb/3bl_ghcd3l5gcp6lxnkzy81h0000gn/T/RtmpjMSWrA/BSgenome.Ainfernus.NCBI.ASM972954v1.Rcheck/00check.log’
#> for details.
#>
#> ── R CMD check results ────────── BSgenome.Ainfernus.NCBI.ASM972954v1 1.0.0 ────
#> Duration: 8.3s
#>
#> ❯ checking whether package ‘BSgenome.Ainfernus.NCBI.ASM972954v1’ can be installed ... ERROR
#> See below...
#>
#> ── Install failure ─────────────────────────────────────────────────────────────
#>
#> * installing *source* package ‘BSgenome.Ainfernus.NCBI.ASM972954v1’ ...
#> ** using staged installation
#> ** R
#> ** byte-compile and prepare package for lazy loading
#> ** help
#> *** installing help indices
#> ** building package indices
#> ** testing if installed package can be loaded from temporary location
#> Error: package or namespace load failed for ‘BSgenome.Ainfernus.NCBI.ASM972954v1’:
#> .onLoad failed in loadNamespace() for 'BSgenome.Ainfernus.NCBI.ASM972954v1', details:
#> call: system.file("extdata", package = pkgname, lib.loc = libname,
#> error: no file found
#> Error: loading failed
#> Execution halted
#> ERROR: loading failed
#> * removing ‘/private/var/folders/xb/3bl_ghcd3l5gcp6lxnkzy81h0000gn/T/RtmpjMSWrA/BSgenome.Ainfernus.NCBI.ASM972954v1.Rcheck/BSgenome.Ainfernus.NCBI.ASM972954v1’
#>
#> 1 error ✖ | 0 warnings ✔ | 0 notes ✔
#> Error: R CMD check found ERRORs
devtools::install_local("BSgenome.Ainfernus.NCBI.ASM972954v1_1.0.0.tar.gz")
#>
#> ── R CMD build ─────────────────────────────────────────────────────────────────
#> * checking for file ‘/private/var/folders/xb/3bl_ghcd3l5gcp6lxnkzy81h0000gn/T/RtmpjMSWrA/remotesa342a261972/BSgenome.Ainfernus.NCBI.ASM972954v1/DESCRIPTION’ ... OK
#> * preparing ‘BSgenome.Ainfernus.NCBI.ASM972954v1’:
#> * checking DESCRIPTION meta-information ... OK
#> * checking for LF line-endings in source and make files and shell scripts
#> * checking for empty or unneeded directories
#> * building ‘BSgenome.Ainfernus.NCBI.ASM972954v1_1.0.0.tar.gz’
#> Warning in i.p(...): installation of package
#> '/var/folders/xb/3bl_ghcd3l5gcp6lxnkzy81h0000gn/T//RtmpjMSWrA/filea343a79169b/BSgenome.Ainfernus.NCBI.ASM972954v1_1.0.0.tar.gz'
#> had non-zero exit status
eval=FALSE
chunks in the vignette instead be evaluated (which might have caught the above issue I had) or does it get a bit circular building/checking/installing another package during the building/checking/installing of BSgenomeForge?BiocCheck::BiocCheck()
suggests Consider adding the maintainer's ORCID iD in 'Authors@R' with 'comment=c(ORCID="...")'
covr::report()
to help identify code that would benefit from unit tests.Received a valid push on git.bioconductor.org; starting a build for commit id: 4874007079d2d70fa17623f2b755b5eff2914a67
Received a valid push on git.bioconductor.org; starting a build for commit id: bbe059e940e8e09ff6efb8159df2f32636483a79
Dear Package contributor,
This is the automated single package builder at bioconductor.org.
Your package has been built on Linux, Mac, and Windows.
On one or more platforms, the build results were: "WARNINGS, ERROR, skipped". This may mean there is a problem with the package that you need to fix. Or it may mean that there is a problem with the build system itself.
Please see the build report for more details. This link will be active for 21 days.
Remember: if you submitted your package after July 7th, 2020,
when making changes to your repository push to
git@git.bioconductor.org:packages/BSgenomeForge
to trigger a new build.
A quick tutorial for setting up remotes and pushing to upstream can be found here.
Dear Package contributor,
This is the automated single package builder at bioconductor.org.
Your package has been built on Linux, Mac, and Windows.
On one or more platforms, the build results were: "WARNINGS, ERROR, skipped". This may mean there is a problem with the package that you need to fix. Or it may mean that there is a problem with the build system itself.
Please see the build report for more details. This link will be active for 21 days.
Remember: if you submitted your package after July 7th, 2020,
when making changes to your repository push to
git@git.bioconductor.org:packages/BSgenomeForge
to trigger a new build.
A quick tutorial for setting up remotes and pushing to upstream can be found here.
Hi @PeteHaitch, Thank you for the initial review. I and @hpages worked on them and I hope the package is in better shape! I am adding comments to all the changes put in place.
[x] Please remove
README-Oct2022.md
from the git repository.
Done.
[x] Is @kakopo or @hpages going to be the maintainer of the package? Please ensure that whoever is maintainer has
"cre"
included as theirrole
in theAuthors@R
field of theDESCRIPTION
(currently it's @hpages).
@hpages shall be the package maintainer.
[x] I think the examples in the
.Rd
files and the vignette should probably setdestdir
=tempdir()
so as not to pollute the user's or build machine's working directory.
Done.
[x] When running the first example from the vignette (actually, all of them) I got a warning that wasn't present in the rendered vignette. What does it mean and should it be addressed?
In my correspondence with @hpages, he mentioned that the warning you get when calling forgeBSgenomeDataPkgFromNCBI()
is probably because you installed BSgenomeForge from a source tarball
obtained without using the --keep-empty-dirs
option.
Perhaps you could try installing the package with this option and see if the same error returns, thanks!
[x] Running
R CMD check
andR CMD install
on theBSgenome.Ainfernus.NCBI.ASM972954v1
example created during the vignette both failed (run via command line or with devtools wrappers). Please clarify why this fails and fix if it should be working.
This seems to fail because of an issue similar to the above. I hope the above solution fits here as well.
[x] Could the
eval=FALSE
chunks in the vignette instead be evaluated (which might have caught the above issue I had) or does it get a bit circular building/checking/installing another package during the building/checking/installing of BSgenomeForge?
The eval=FALSE
chunks were not evaluated as they do the circular building/checking/installing of BSgenomeForge, so it was best to leave them unchecked.
[x] Please add an Installation section to the vignette (https://contributions.bioconductor.org/docs.html?vignettes#installation)
Done.
[x]
BiocCheck::BiocCheck()
suggestsConsider adding the maintainer's ORCID iD in 'Authors@R' with 'comment=c(ORCID="...")'
Neither @hpages nor I have an ORCID.
[x] Consider adding a package-level man page (https://contributions.bioconductor.org/docs.html?vignettes#package-level-documentation)
This was not added.
[x] Consider adding some more unit tests. You could take a look at running covr::report() to help identify code that would benefit from unit tests.
Done.
Thank you for making the required changes, @kakopo and @hpages. I'm now happy to accept BSgenomeForge into Bioconductor. Congratulations and thank you for your contribution!
I can confirm that building the package with R CMD build --keep-empty-dirs
eliminated the extraneous warning in the vignette and in checking and installing the example packages from the vignette.
Sorry, before I can formally accept the package could you please try please push to git@git.bioconductor.org:packages/BSgenomeForge
to trigger a new build.
The most recent build (https://github.com/Bioconductor/Contributions/issues/2943#issuecomment-1488062691) returned an error on macOS (merida1
), although the package passes checks on my personal macOS (Apple silicon) device.
@PeteHaitch The mac builder is still down. if it is building on linux and your local mac I would use those right now for reference.
Your package has been accepted. It will be added to the Bioconductor nightly builds.
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