vignettes/bioc.Rmd
bioc.RmdThis vignette discusses processes that can be undertaken to bring MRCIEU packages into the Bioconductor ecosystem.
The Bioconductor website pages for package submission provide full details.
Submit by opening a new issue in the Bioconductor Contributions repository, following the guidelines of the README.md file. Assuming that your package is in a GitHub Repository and under the default branch, add the link to your repository to the issue you are opening. You cannot specify any alternative branches; the default branch is utilized. The default branch must contain only package code. Any files or directories for other applications (Github Actions, devtool, etc) should be in a different branch.
The package will be submitted to the Bioconductor build system (BBS). The system will check out your package from GitHub. It will then run R CMD build to create a ‘tarball’ of your source code, vignettes, and man pages. It will run R CMD check on the tarball, to ensure that the package conforms to standard R programming best practices. Bioconductor has chosen to utilize a custom R CMD check environment; See R CMD check environment for more details. Finally, the build system will run BiocCheckGitClone() and BiocCheck() to ensure that the package conforms to Bioconductor BiocCheck standards. The system will perform these steps using the ‘devel’ version of Bioconductor, on three platforms (Linux, Mac OS X, and Windows). After these steps are complete, a link to a build report will be appended to the new package issue. Avoid surprises by running these checks on your own computer, under the ‘devel’ version of Bioconductor, before submitting your package.
For submission to Bioconductor 3.14, it would be good to start a submission in September. We use R 4.1.1 with BiocManager::version() returning ‘3.14’ and BiocManager::valid() returning ‘TRUE’.
ieugwasr
As of Sept 18, there is a bug in BiocCheck, a key QC component for the submission process. For now I am using the vjcitn-patch-1 branch of BiocCheck at github.com/vjcitn/BiocCheck.
My sense is that the server is reliable enough to use directly in the vignette. Thus this WARNING should be solved, and the following NOTE:
* WARNING: Evaluate more vignette chunks.
# of code chunks: 40
# of eval=FALSE: 0
# of nonexecutable code chunks by syntax: 29
# total unevaluated 29 (72%)
* NOTE: 'sessionInfo' not found in vignette(s)
Missing from file(s):
vignettes/guide.Rmd
vignettes/local_ld.Rmd
vignettes/timings.Rmd* Checking coding practice...
* NOTE: Avoid sapply(); use vapply()
Found in files:
afl2.r (line 88, column 16)
query.R (line 188, column 9)
* NOTE: Avoid 1:...; use seq_len() or seq_along()
Found in files:
backwards.R (line 16, column 18)
ld_clump.R (line 58, column 18)
ld_clump.R (line 154, column 27)
ld_clump.R (line 155, column 19)
variants.R (line 17, column 18)
zzz.R (line 20, column 41)
* NOTE: Avoid redundant 'stop' and 'warn*' in signal conditions
Found in files:
/Users/vincentcarey/MRCIEU/ieugwasr/R/query.R (line 87, column
25)
/Users/vincentcarey/MRCIEU/ieugwasr/R/query.R (line 88, column
25)
/Users/vincentcarey/MRCIEU/ieugwasr/R/query.R (line 95, column
30)
/Users/vincentcarey/MRCIEU/ieugwasr/R/query.R (line 97, column
30)
* WARNING: Avoid T/F variables; If logical, use TRUE/FALSE (found 8
times)
T in R/ld_clump.R (line 130, column 101)
T in R/ld_clump.R (line 142, column 65)
F in R/ld_clump.R (line 130, column 88)
F in R/ld_clump.R (line 130, column 110)
F in R/ld_matrix.R (line 82, column 62)
F in R/ld_matrix.R (line 82, column 75)
F in R/ld_matrix.R (line 82, column 84)
T in R/zzz.R (line 20, column 79)
* WARNING: Avoid class membership checks with class() / is() and ==
/ !=; Use is(x, 'class') for S4 classes
Found in files:
afl2.r (line 38, column 23)
afl2.r (line 58, column 23)
query.R (line 231, column 23)
query.R (line 298, column 23)
query.R (line 351, column 23)
variants.R (line 21, column 29)* Checking man page documentation...
* WARNING: Add non-empty \value sections to the following man
pages: man/ld_clump_api.Rd, man/logging_info.Rd, man/pipe.Rd,
man/revoke_access_token.Rd, man/select_api.Rd
* ERROR: At least 80% of man pages documenting exported objects
must have runnable examples. The following pages do not:
afl2_chrpos.Rd, afl2_list.Rd, afl2_rsid.Rd, api_query.Rd,
api_status.Rd, associations.Rd, batch_from_id.Rd, batches.Rd,
check_access_token.Rd, cor.Rd, editcheck.Rd, fill_n.Rd,
get_access_token.Rd, get_query_content.Rd, gwasinfo.Rd,
infer_ancestry.Rd, ld_clump_local.Rd, ld_clump.Rd,
ld_matrix_local.Rd, ld_matrix.Rd, ld_reflookup.Rd, legacy_ids.Rd,
logging_info.Rd, phewas.Rd, pipe.Rd, revoke_access_token.Rd,
select_api.Rd, tophits.Rd, variants_chrpos.Rd, variants_gene.Rd,
variants_rsid.Rd, variants_to_rsid.Rd* Checking for support site registration...
Maintainer is registered at support site.
* ERROR: Maintainer must add package name to Watched Tags on the
support site; Edit your Support Site User Profile to add Watched
Tags.
Summary:
ERROR count: 3
WARNING count: 6
NOTE count: 12
For detailed information about these checks, see the BiocCheck
vignette, available at
https://bioconductor.org/packages/3.14/bioc/vignettes/BiocCheck/inst/doc/BiocCheck.html#interpreting-bioccheck-output
BiocCheck FAILED.* checking dependencies in R code ... WARNING
Namespaces in Imports field not imported from:
‘Rhtslib’ ‘coloc’ ‘jsonlite’ ‘methods’ ‘testthat’ ‘tidyr’
All declared Imports should be used.* Checking coding practice...
* NOTE: Avoid sapply(); use vapply()
Found in files:
binaries.r (line 20, column 26)
binaries.r (line 49, column 26)
query.r (line 149, column 18)
query.r (line 150, column 16)
query.r (line 155, column 20)
query.r (line 156, column 20)
* NOTE: Avoid 1:...; use seq_len() or seq_along()
Found in files:
manipulate.r (line 98, column 26)
manipulate.r (line 213, column 35)
query.r (line 393, column 53)
* WARNING: Avoid T/F variables; If logical, use TRUE/FALSE (found
15 times)
F in R/proxy.r (line 28, column 92)
F in R/proxy.r (line 28, column 99)
F in R/proxy.r (line 28, column 105)
F in R/query.r (line 338, column 76)
F in R/query.r (line 338, column 83)
F in R/query.r (line 338, column 89)
F in R/query.r (line 393, column 103)
F in R/query.r (line 393, column 110)
F in R/query.r (line 393, column 116)
F in R/rsid_index.r (line 22, column 62)
F in R/rsid_index.r (line 22, column 69)
F in R/rsid_index.r (line 22, column 75)
F in R/rsid_index.r (line 96, column 71)
F in R/rsid_index.r (line 96, column 78)
F in R/rsid_index.r (line 96, column 84)
* WARNING: Avoid class membership checks with class() / is() and ==
/ !=; Use is(x, 'class') for S4 classes
Found in files:
manipulate.r (line 225, column 37)
* ERROR: Avoid references to external hosting platforms
Found in files:
binaries.r (line 78, column 30)
binaries.r (line 105, column 30)* Checking man page documentation...
* WARNING: Add non-empty \value sections to the following man
pages: man/create_ldref_sqlite.Rd,
man/create_rsidx_index_from_vcf.Rd, man/pipe.Rd
* ERROR: At least 80% of man pages documenting exported objects
must have runnable examples. The following pages do not:
check_bcftools.Rd, check_plink.Rd, create_ldref_sqlite.Rd,
create_rsidx_index_from_vcf.Rd, create_rsidx_sub_index.Rd,
create_vcf.Rd, get_ld_proxies.Rd, merge_vcf.Rd, parse_chrompos.Rd,
pipe.Rd, proxy_match.Rd, query_chrompos_bcftools.Rd,
query_chrompos_file.Rd, query_chrompos_vcf.Rd, query_gwas.Rd,
query_pval_bcftools.Rd, query_pval_file.Rd, query_pval_vcf.Rd,
query_rsid_bcftools.Rd, query_rsid_file.Rd, query_rsid_rsidx.Rd,
query_rsid_vcf.Rd, query_rsidx.Rd, set_bcftools.Rd, set_plink.Rd,
sqlite_ld_proxies.Rd, vcf_to_granges.Rd, vcf_to_tibble.Rd,
vcflist_overlaps.Rd
* Checking package NEWS...
* NOTE: Consider adding a NEWS file, so your package news will be
included in Bioconductor release announcements.