Error in Bioc check

[gabrielodom]

Hi Tiago,
Our build is currently failing: http://bioconductor.org/checkResults/devel/bioc-LATEST/coMethDMR/nebbiolo1-checksrc.html
The issue is that tail() is not imported from the utils:: namespace to ours. Can you please add this dependency? Code in question below:

coMethDMR/R/zzz.R

Line 41 in 0c06d01

tail(names(res[res$title == char,]),1)

@fveitz, when Tiago is finished, please check the package again, increment to version 0.99.17 (to trigger a new build), and push to Bioconductor?

thank you both!

[fveitz]

Hi Gabriel and Tiago, Yes, sure. Just let me know when it's ready and I will do it on my end. Thank you.

…

On Mon, Apr 4, 2022 at 2:46 PM Gabriel J. Odom ***@***.***> wrote: Assigned #21 <#21> to @fveitz <https://github.com/fveitz>. — Reply to this email directly, view it on GitHub <#21 (comment)>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/ASCHHMUFC7B4QN63IODBLSLVDM2JBANCNFSM5SQNMCJQ> . You are receiving this because you were assigned.Message ID: ***@***.***>

[tiagochst]

I sent the updates and ran check on my end. It passed for me. On Mon, Apr 4, 2022, 5:15 PM Fernanda Veitzman ***@***.***> wrote:

…

Hi Gabriel and Tiago, Yes, sure. Just let me know when it's ready and I will do it on my end. Thank you. On Mon, Apr 4, 2022 at 2:46 PM Gabriel J. Odom ***@***.***> wrote: > Assigned #21 <#21> to > @fveitz <https://github.com/fveitz>. > > — > Reply to this email directly, view it on GitHub > <#21 (comment) >, > or unsubscribe > < https://github.com/notifications/unsubscribe-auth/ASCHHMUFC7B4QN63IODBLSLVDM2JBANCNFSM5SQNMCJQ > > . > You are receiving this because you were assigned.Message ID: > ***@***.***> > — Reply to this email directly, view it on GitHub <#21 (comment)>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/AABDQ6POKKMK257QQRSM5B3VDNLXBANCNFSM5SQNMCJQ> . You are receiving this because you were assigned.Message ID: ***@***.***>

[fveitz]

I have just checked it, please find below the output: Error: .onLoad failed in loadNamespace() for 'coMethDMR', details: call: tail(names(res[res$title == char, ]), 1) error: could not find function "tail" Execution halted 0 errors ✓ | 2 warnings x | 3 notes xError: R CMD check found WARNINGsExecution halted Exited with status 1. On Mon, Apr 4, 2022 at 6:08 PM Tiago Chedraoui Silva < ***@***.***> wrote:

…

I sent the updates and ran check on my end. It passed for me. On Mon, Apr 4, 2022, 5:15 PM Fernanda Veitzman ***@***.***> wrote: > Hi Gabriel and Tiago, > Yes, sure. > Just let me know when it's ready and I will do it on my end. > Thank you. > > > On Mon, Apr 4, 2022 at 2:46 PM Gabriel J. Odom ***@***.***> > wrote: > > > Assigned #21 <#21> to > > @fveitz <https://github.com/fveitz>. > > > > — > > Reply to this email directly, view it on GitHub > > < #21 (comment) > >, > > or unsubscribe > > < > https://github.com/notifications/unsubscribe-auth/ASCHHMUFC7B4QN63IODBLSLVDM2JBANCNFSM5SQNMCJQ > > > > . > > You are receiving this because you were assigned.Message ID: > > ***@***.***> > > > > — > Reply to this email directly, view it on GitHub > < #21 (comment) >, > or unsubscribe > < https://github.com/notifications/unsubscribe-auth/AABDQ6POKKMK257QQRSM5B3VDNLXBANCNFSM5SQNMCJQ > > . > You are receiving this because you were assigned.Message ID: > ***@***.***> > — Reply to this email directly, view it on GitHub <#21 (comment)>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/ASCHHMXLHKXDIKWBNSZSSGLVDNR7BANCNFSM5SQNMCJQ> . You are receiving this because you were mentioned.Message ID: ***@***.***>

[tiagochst]

It was in the wrong branch. Now it is in the master On Mon, Apr 4, 2022, 7:13 PM Fernanda Veitzman ***@***.***> wrote:

…

I have just checked it, please find below the output: Error: .onLoad failed in loadNamespace() for 'coMethDMR', details: call: tail(names(res[res$title == char, ]), 1) error: could not find function "tail" Execution halted 0 errors ✓ | 2 warnings x | 3 notes xError: R CMD check found WARNINGsExecution halted Exited with status 1. On Mon, Apr 4, 2022 at 6:08 PM Tiago Chedraoui Silva < ***@***.***> wrote: > I sent the updates and ran check on my end. It passed for me. > > On Mon, Apr 4, 2022, 5:15 PM Fernanda Veitzman ***@***.***> > wrote: > > > Hi Gabriel and Tiago, > > Yes, sure. > > Just let me know when it's ready and I will do it on my end. > > Thank you. > > > > > > On Mon, Apr 4, 2022 at 2:46 PM Gabriel J. Odom ***@***.***> > > wrote: > > > > > Assigned #21 <#21 > > to > > > @fveitz <https://github.com/fveitz>. > > > > > > — > > > Reply to this email directly, view it on GitHub > > > < > #21 (comment) > > >, > > > or unsubscribe > > > < > > > https://github.com/notifications/unsubscribe-auth/ASCHHMUFC7B4QN63IODBLSLVDM2JBANCNFSM5SQNMCJQ > > > > > > . > > > You are receiving this because you were assigned.Message ID: > > > ***@***.***> > > > > > > > — > > Reply to this email directly, view it on GitHub > > < > #21 (comment) > >, > > or unsubscribe > > < > https://github.com/notifications/unsubscribe-auth/AABDQ6POKKMK257QQRSM5B3VDNLXBANCNFSM5SQNMCJQ > > > > . > > You are receiving this because you were assigned.Message ID: > > ***@***.***> > > > > — > Reply to this email directly, view it on GitHub > < #21 (comment) >, > or unsubscribe > < https://github.com/notifications/unsubscribe-auth/ASCHHMXLHKXDIKWBNSZSSGLVDNR7BANCNFSM5SQNMCJQ > > . > You are receiving this because you were mentioned.Message ID: > ***@***.***> > — Reply to this email directly, view it on GitHub <#21 (comment)>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/AABDQ6NHI3TKP4MTLNADESLVDNZSBANCNFSM5SQNMCJQ> . You are receiving this because you were assigned.Message ID: ***@***.***>

[fveitz]

Hi Gabriel and Tiago, Please find below the check output. Can I push upstream? ==> devtools::check(document = FALSE) ── Building ────────────────────────────────────────────────────────────────────── coMethDMR ──Setting env vars: • CFLAGS : -Wall -pedantic -fdiagnostics-color=always • CXXFLAGS : -Wall -pedantic -fdiagnostics-color=always • CXX11FLAGS: -Wall -pedantic -fdiagnostics-color=always───────────────────────────────────────────────────────────────────────────────────────────────✓ checking for file ‘/Users/fernandaveitzman/Documents/GitHub/coMethDMR/DESCRIPTION’ ...─ preparing ‘coMethDMR’:✓ checking DESCRIPTION meta-information ...─ installing the package to build vignettes✓ creating vignettes (3m 44s)─ checking for LF line-endings in source and make files and shell scripts─ checking for empty or unneeded directories─ looking to see if a ‘data/datalist’ file should be added─ building ‘coMethDMR_0.99.17.tar.gz’ ── Checking ────────────────────────────────────────────────────────────────────── coMethDMR ──Setting env vars: • _R_CHECK_CRAN_INCOMING_REMOTE_: FALSE • _R_CHECK_CRAN_INCOMING_ : FALSE • _R_CHECK_FORCE_SUGGESTS_ : FALSE • NOT_CRAN : true── R CMD check ────────────────────────────────────────────────────────────────── using log directory ‘/Users/fernandaveitzman/Documents/GitHub/coMethDMR.Rcheck’─ using R version 4.1.0 (2021-05-18)─ using platform: x86_64-apple-darwin17.0 (64-bit)─ using session charset: UTF-8─ using options ‘--no-manual --as-cran’✓ checking for file ‘coMethDMR/DESCRIPTION’─ this is package ‘coMethDMR’ version ‘0.99.17’─ package encoding: UTF-8✓ checking package namespace informationN checking package dependencies (7.6s) Package suggested but not available for checking: ‘IlluminaHumanMethylationEPICanno.ilm10b4.hg19’✓ checking if this is a source package✓ checking if there is a namespace✓ checking for executable files (611ms)✓ checking for hidden files and directories✓ checking for portable file names ...✓ checking for sufficient/correct file permissions✓ checking whether package ‘coMethDMR’ can be installed (30.5s)✓ checking installed package size ...✓ checking package directory ...✓ checking for future file timestamps (464ms)✓ checking ‘build’ directory✓ checking DESCRIPTION meta-information ...✓ checking top-level files✓ checking for left-over files✓ checking index information ...W checking package subdirectories ... Subdirectory 'man' contains invalid file names: ‘.AnnotateResults 2.Rd.icloud’ ‘.pheno_df 2.Rd.icloud’ Please remove or rename the files. See section ‘Package subdirectories’ in the ‘Writing R Extensions’ manual.✓ checking R files for non-ASCII characters ...✓ checking R files for syntax errors ...✓ checking whether the package can be loaded (11.2s)✓ checking whether the package can be loaded with stated dependencies (10.6s)✓ checking whether the package can be unloaded cleanly (10.5s)✓ checking whether the namespace can be loaded with stated dependencies (10.6s)✓ checking whether the namespace can be unloaded cleanly (10.8s)✓ checking dependencies in R code (12.4s)✓ checking S3 generic/method consistency (12s)✓ checking replacement functions (10.6s)✓ checking foreign function calls (9.9s)N checking R code for possible problems (43.4s) File ‘coMethDMR/R/zzz.R’: .onLoad calls: packageStartupMessage("Checking for cached SeSAMe data.") packageStartupMessage("Caching SeSAMe data for 450k/EPIC arrays.") See section ‘Good practice’ in '?.onAttach'.✓ checking Rd files ...✓ checking Rd metadata ...✓ checking Rd line widths ...✓ checking Rd cross-references ...✓ checking for missing documentation entries (10.4s)✓ checking for code/documentation mismatches (31.1s)✓ checking Rd \usage sections (11.1s)✓ checking Rd contents ...✓ checking for unstated dependencies in examples ...✓ checking contents of ‘data’ directory (1.2s)✓ checking data for non-ASCII characters ...✓ checking data for ASCII and uncompressed saves ...✓ checking installed files from ‘inst/doc’ ...✓ checking files in ‘vignettes’ ...✓ checking examples (3m 10.4s) Examples with CPU (user + system) or elapsed time > 5s user system elapsed CoMethSingleRegion 23.737 0.434 28.098 lmmTest 17.996 0.323 21.091 lmmTestAllRegions 15.043 0.227 17.019 CpGsInfoOneRegion 13.553 0.259 15.941 SplitCpGDFbyRegion 13.510 0.248 16.399 CoMethAllRegions 9.180 0.137 10.163 GetCpGsInRegion 8.688 0.135 10.644 AnnotateResults 7.321 0.339 7.667 CloseBySingleRegion 5.241 0.223 6.382 CpGsInfoAllRegions 4.916 0.112 6.197 CreateOutputDF 4.527 0.084 5.266 OrderCpGsByLocation 4.391 0.077 5.317 ImportSesameData 4.349 0.068 5.131✓ checking for unstated dependencies in ‘tests’ ...─ checking tests ...✓ Running ‘testthat 2.R’✓ Running ‘testthat.R’ [67s/74s] (1m 14.2s)✓ checking for unstated dependencies in vignettes (1m 14.4s)W checking package vignettes in ‘inst/doc’ Failed to locate ‘weave’ output file ‘vin1_Introduction_to_coMethDMR_geneBasedPipeline 2.pdf’ or ‘vin1_Introduction_to_coMethDMR_geneBasedPipeline 2.html’ for vignette with name ‘vin1_Introduction_to_coMethDMR_geneBasedPipeline 2’ and engine ‘knitr::rmarkdown’. The following files exist in working directory ‘/Users/fernandaveitzman/Documents/GitHub/coMethDMR.Rcheck/00_pkg_src/coMethDMR/inst/doc’: ‘vin1_Introduction_to_coMethDMR_geneBasedPipeline 2.R’ (NA bytes), ‘vin1_Introduction_to_coMethDMR_geneBasedPipeline.R’ (NA bytes), ‘vin1_Introduction_to_coMethDMR_geneBasedPipeline.Rmd’ (NA bytes), ‘vin1_Introduction_to_coMethDMR_geneBasedPipeline.html’ (NA bytes), ‘vin2_BiocParallel_for_coMethDMR_geneBasedPipeline.R’ (NA bytes), ‘vin2_BiocParallel_for_coMethDMR_geneBasedPipeline.Rmd’ (NA bytes), ‘vin2_BiocParallel_for_coMethDMR_geneBasedPipeline.html’ (NA bytes)Failed to locate ‘weave’ output file ‘vin2_BiocParallel_for_coMethDMR_geneBasedPipeline 2.pdf’ or ‘vin2_BiocParallel_for_coMethDMR_geneBasedPipeline 2.html’ for vignette with name ‘vin2_BiocParallel_for_coMethDMR_geneBasedPipeline 2’ and engine ‘knitr::rmarkdown’. The following files exist in working directory ‘/Users/fernandaveitzman/Documents/GitHub/coMethDMR.Rcheck/00_pkg_src/coMethDMR/inst/doc’: ‘vin1_Introduction_to_coMethDMR_geneBasedPipeline 2.R’ (NA bytes), ‘vin1_Introduction_to_coMethDMR_geneBasedPipeline.R’ (NA bytes), ‘vin1_Introduction_to_coMethDMR_geneBasedPipeline.Rmd’ (NA bytes), ‘vin1_Introduction_to_coMethDMR_geneBasedPipeline.html’ (NA bytes), ‘vin2_BiocParallel_for_coMethDMR_geneBasedPipeline.R’ (NA bytes), ‘vin2_BiocParallel_for_coMethDMR_geneBasedPipeline.Rmd’ (NA bytes), ‘vin2_BiocParallel_for_coMethDMR_geneBasedPipeline.html’ (NA bytes) Package vignettes without corresponding single PDF/HTML: ‘vin1_Introduction_to_coMethDMR_geneBasedPipeline 2.Rmd’ ‘vin2_BiocParallel_for_coMethDMR_geneBasedPipeline 2.Rmd’ W checking re-building of vignette outputs (6m 15.2s) Error(s) in re-building vignettes: duplicated vignette titles: ‘"Introduction to coMethDMR"’ ‘"coMethDMR with Parallel Computing"’

--- re-building ‘vin1_Introduction_to_coMethDMR_geneBasedPipeline 2.Rmd’ using rmarkdown Checking for cached SeSAMe data. snapshotDate(): 2021-05-18 Loading required package: corrplot corrplot 0.89 loaded snapshotDate(): 2021-05-18 see ?sesameData and browseVignettes('sesameData') for documentation Setting options('download.file.method.GEOquery'='auto') Setting options('GEOquery.inmemory.gpl'=FALSE) snapshotDate(): 2021-05-18 see ?sesameData and browseVignettes('sesameData') for documentation Analyzing region chr22:17565612-17565675. For future calls to this function, perhaps specify a log file. Set the file name of the log file with the outLogFile argument. snapshotDate(): 2021-05-18 see ?sesameData and browseVignettes('sesameData') for documentation snapshotDate(): 2021-05-18 see ?sesameData and browseVignettes('sesameData') for documentation snapshotDate(): 2021-05-18 see ?sesameData and browseVignettes('sesameData') for documentation snapshotDate(): 2021-05-18 see ?sesameData and browseVignettes('sesameData') for documentation Error: processing vignette 'vin1_Introduction_to_coMethDMR_geneBasedPipeline 2.Rmd' failed with diagnostics: Failed to locate ‘weave’ output file ‘vin1_Introduction_to_coMethDMR_geneBasedPipeline 2.pdf’ or ‘vin1_Introduction_to_coMethDMR_geneBasedPipeline 2.html’ for vignette with name ‘vin1_Introduction_to_coMethDMR_geneBasedPipeline 2’ and engine ‘knitr::rmarkdown’. The following files exist in working directory ‘/Users/fernandaveitzman/Documents/GitHub/coMethDMR.Rcheck/vign_test/coMethDMR/vignettes’: ‘vin1_Introduction_to_coMethDMR_geneBasedPipeline 2.Rmd’ (18385 bytes), ‘vin1_Introduction_to_coMethDMR_geneBasedPipeline-2.R’ (7016 bytes), ‘vin1_Introduction_to_coMethDMR_geneBasedPipeline-2.html’ (861577 bytes), ‘vin1_Introduction_to_coMethDMR_geneBasedPipeline.Rmd’ (18385 bytes), ‘vin2_BiocParallel_for_coMethDMR_geneBasedPipeline 2.Rmd’ (10361 bytes), ‘vin2_BiocParallel_for_coMethDMR_geneBasedPipeline.Rmd’ (10361 bytes) --- failed re-building ‘vin1_Introduction_to_coMethDMR_geneBasedPipeline 2.Rmd’

--- re-building ‘vin1_Introduction_to_coMethDMR_geneBasedPipeline.Rmd’ using rmarkdown Checking for cached SeSAMe data. snapshotDate(): 2021-05-18 Loading required package: corrplot corrplot 0.89 loaded snapshotDate(): 2021-05-18 see ?sesameData and browseVignettes('sesameData') for documentation Setting options('download.file.method.GEOquery'='auto') Setting options('GEOquery.inmemory.gpl'=FALSE) snapshotDate(): 2021-05-18 see ?sesameData and browseVignettes('sesameData') for documentation Analyzing region chr22:17565612-17565675. For future calls to this function, perhaps specify a log file. Set the file name of the log file with the outLogFile argument. snapshotDate(): 2021-05-18 see ?sesameData and browseVignettes('sesameData') for documentation snapshotDate(): 2021-05-18 see ?sesameData and browseVignettes('sesameData') for documentation snapshotDate(): 2021-05-18 see ?sesameData and browseVignettes('sesameData') for documentation snapshotDate(): 2021-05-18 see ?sesameData and browseVignettes('sesameData') for documentation --- finished re-building ‘vin1_Introduction_to_coMethDMR_geneBasedPipeline.Rmd’

--- re-building ‘vin2_BiocParallel_for_coMethDMR_geneBasedPipeline 2.Rmd’ using rmarkdown Checking for cached SeSAMe data. snapshotDate(): 2021-05-18 snapshotDate(): 2021-05-18 see ?sesameData and browseVignettes('sesameData') for documentation snapshotDate(): 2021-05-18 see ?sesameData and browseVignettes('sesameData') for documentation Analyzing region chr22:30901532-30901886. Analyzing region chr22:39883190-39883347. Analyzing region chr22:30662799-30663041. Analyzing region chr22:43253521-43253559. For future calls to this function, perhaps specify a log file. Set the file name of the log file with the outLogFile argument. Error: processing vignette 'vin2_BiocParallel_for_coMethDMR_geneBasedPipeline 2.Rmd' failed with diagnostics: Failed to locate ‘weave’ output file ‘vin2_BiocParallel_for_coMethDMR_geneBasedPipeline 2.pdf’ or ‘vin2_BiocParallel_for_coMethDMR_geneBasedPipeline 2.html’ for vignette with name ‘vin2_BiocParallel_for_coMethDMR_geneBasedPipeline 2’ and engine ‘knitr::rmarkdown’. The following files exist in working directory ‘/Users/fernandaveitzman/Documents/GitHub/coMethDMR.Rcheck/vign_test/coMethDMR/vignettes’: ‘vin1_Introduction_to_coMethDMR_geneBasedPipeline 2.Rmd’ (18385 bytes), ‘vin1_Introduction_to_coMethDMR_geneBasedPipeline-2.R’ (7016 bytes), ‘vin1_Introduction_to_coMethDMR_geneBasedPipeline-2.html’ (861577 bytes), ‘vin1_Introduction_to_coMethDMR_geneBasedPipeline.R’ (7016 bytes), ‘vin1_Introduction_to_coMethDMR_geneBasedPipeline.Rmd’ (18385 bytes), ‘vin1_Introduction_to_coMethDMR_geneBasedPipeline.html’ (861577 bytes), ‘vin2_BiocParallel_for_coMethDMR_geneBasedPipeline 2.Rmd’ (10361 bytes), ‘vin2_BiocParallel_for_coMethDMR_geneBasedPipeline-2.R’ (3617 bytes), ‘vin2_BiocParallel_for_coMethDMR_geneBasedPipeline-2.html’ (768223 bytes), ‘vin2_BiocParallel_for_coMethDMR_geneBasedPipeline.Rmd’ (10361 bytes) --- failed re-building ‘vin2_BiocParallel_for_coMethDMR_geneBasedPipeline 2.Rmd’

--- re-building ‘vin2_BiocParallel_for_coMethDMR_geneBasedPipeline.Rmd’ using rmarkdown Checking for cached SeSAMe data. snapshotDate(): 2021-05-18 snapshotDate(): 2021-05-18 see ?sesameData and browseVignettes('sesameData') for documentation snapshotDate(): 2021-05-18 see ?sesameData and browseVignettes('sesameData') for documentation Analyzing region chr22:30901532-30901886. Analyzing region chr22:39883190-39883347. Analyzing region chr22:30662799-30663041. Analyzing region chr22:43253521-43253559. For future calls to this function, perhaps specify a log file. Set the file name of the log file with the outLogFile argument. --- finished re-building ‘vin2_BiocParallel_for_coMethDMR_geneBasedPipeline.Rmd’ SUMMARY: processing the following files failed: ‘vin1_Introduction_to_coMethDMR_geneBasedPipeline 2.Rmd’ ‘vin2_BiocParallel_for_coMethDMR_geneBasedPipeline 2.Rmd’ Error: Vignette re-building failed. Error: Duplicate vignette titles. Ensure that the %\VignetteIndexEntry lines in the vignette sources correspond to the vignette titles. Execution halted ✓ checking for non-standard things in the check directory✓ checking for detritus in the temp directory See ‘/Users/fernandaveitzman/Documents/GitHub/coMethDMR.Rcheck/00check.log’ for details. ── R CMD check results ────────────────────────────────── coMethDMR 0.99.17 ──── Duration: 14m 38.3s

checking package subdirectories ... WARNING

Subdirectory 'man' contains invalid file names: ‘.AnnotateResults 2.Rd.icloud’ ‘.pheno_df 2.Rd.icloud’ Please remove or rename the files. See section ‘Package subdirectories’ in the ‘Writing R Extensions’ manual.

checking package vignettes in ‘inst/doc’ ... WARNING

Failed to locate ‘weave’ output file ‘vin1_Introduction_to_coMethDMR_geneBasedPipeline 2.pdf’ or ‘vin1_Introduction_to_coMethDMR_geneBasedPipeline 2.html’ for vignette with name ‘vin1_Introduction_to_coMethDMR_geneBasedPipeline 2’ and engine ‘knitr::rmarkdown’. The following files exist in working directory ‘/Users/fernandaveitzman/Documents/GitHub/coMethDMR.Rcheck/00_pkg_src/coMethDMR/inst/doc’: ‘vin1_Introduction_to_coMethDMR_geneBasedPipeline 2.R’ (NA bytes), ‘vin1_Introduction_to_coMethDMR_geneBasedPipeline.R’ (NA bytes), ‘vin1_Introduction_to_coMethDMR_geneBasedPipeline.Rmd’ (NA bytes), ‘vin1_Introduction_to_coMethDMR_geneBasedPipeline.html’ (NA bytes), ‘vin2_BiocParallel_for_coMethDMR_geneBasedPipeline.R’ (NA bytes), ‘vin2_BiocParallel_for_coMethDMR_geneBasedPipeline.Rmd’ (NA bytes), ‘vin2_BiocParallel_for_coMethDMR_geneBasedPipeline.html’ (NA bytes)Failed to locate ‘weave’ output file ‘vin2_BiocParallel_for_coMethDMR_geneBasedPipeline 2.pdf’ or ‘vin2_BiocParallel_for_coMethDMR_geneBasedPipeline 2.html’ for vignette with name ‘vin2_BiocParallel_for_coMethDMR_geneBasedPipeline 2’ and engine ‘knitr::rmarkdown’. The following files exist in working directory ‘/Users/fernandaveitzman/Documents/GitHub/coMethDMR.Rcheck/00_pkg_src/coMethDMR/inst/doc’: ‘vin1_Introduction_to_coMethDMR_geneBasedPipeline 2.R’ (NA bytes), ‘vin1_Introduction_to_coMethDMR_geneBasedPipeline.R’ (NA bytes), ‘vin1_Introduction_to_coMethDMR_geneBasedPipeline.Rmd’ (NA bytes), ‘vin1_Introduction_to_coMethDMR_geneBasedPipeline.html’ (NA bytes), ‘vin2_BiocParallel_for_coMethDMR_geneBasedPipeline.R’ (NA bytes), ‘vin2_BiocParallel_for_coMethDMR_geneBasedPipeline.Rmd’ (NA bytes), ‘vin2_BiocParallel_for_coMethDMR_geneBasedPipeline.html’ (NA bytes) Package vignettes without corresponding single PDF/HTML: ‘vin1_Introduction_to_coMethDMR_geneBasedPipeline 2.Rmd’ ‘vin2_BiocParallel_for_coMethDMR_geneBasedPipeline 2.Rmd’

checking re-building of vignette outputs ... WARNING

Error(s) in re-building vignettes: duplicated vignette titles: ‘"Introduction to coMethDMR"’ ‘"coMethDMR with Parallel Computing"’

--- re-building ‘vin1_Introduction_to_coMethDMR_geneBasedPipeline 2.Rmd’ using rmarkdown Checking for cached SeSAMe data. snapshotDate(): 2021-05-18 Loading required package: corrplot corrplot 0.89 loaded snapshotDate(): 2021-05-18 see ?sesameData and browseVignettes('sesameData') for documentation Setting options('download.file.method.GEOquery'='auto') Setting options('GEOquery.inmemory.gpl'=FALSE) snapshotDate(): 2021-05-18 see ?sesameData and browseVignettes('sesameData') for documentation Analyzing region chr22:17565612-17565675. For future calls to this function, perhaps specify a log file. Set the file name of the log file with the outLogFile argument. snapshotDate(): 2021-05-18 see ?sesameData and browseVignettes('sesameData') for documentation snapshotDate(): 2021-05-18 see ?sesameData and browseVignettes('sesameData') for documentation snapshotDate(): 2021-05-18 see ?sesameData and browseVignettes('sesameData') for documentation snapshotDate(): 2021-05-18 see ?sesameData and browseVignettes('sesameData') for documentation Error: processing vignette 'vin1_Introduction_to_coMethDMR_geneBasedPipeline 2.Rmd' failed with diagnostics: Failed to locate ‘weave’ output file ‘vin1_Introduction_to_coMethDMR_geneBasedPipeline 2.pdf’ or ‘vin1_Introduction_to_coMethDMR_geneBasedPipeline 2.html’ for vignette with name ‘vin1_Introduction_to_coMethDMR_geneBasedPipeline 2’ and engine ‘knitr::rmarkdown’. The following files exist in working directory ‘/Users/fernandaveitzman/Documents/GitHub/coMethDMR.Rcheck/vign_test/coMethDMR/vignettes’: ‘vin1_Introduction_to_coMethDMR_geneBasedPipeline 2.Rmd’ (18385 bytes), ‘vin1_Introduction_to_coMethDMR_geneBasedPipeline-2.R’ (7016 bytes), ‘vin1_Introduction_to_coMethDMR_geneBasedPipeline-2.html’ (861577 bytes), ‘vin1_Introduction_to_coMethDMR_geneBasedPipeline.Rmd’ (18385 bytes), ‘vin2_BiocParallel_for_coMethDMR_geneBasedPipeline 2.Rmd’ (10361 bytes), ‘vin2_BiocParallel_for_coMethDMR_geneBasedPipeline.Rmd’ (10361 bytes) --- failed re-building ‘vin1_Introduction_to_coMethDMR_geneBasedPipeline 2.Rmd’

--- re-building ‘vin1_Introduction_to_coMethDMR_geneBasedPipeline.Rmd’ using rmarkdown Checking for cached SeSAMe data. snapshotDate(): 2021-05-18 Loading required package: corrplot corrplot 0.89 loaded snapshotDate(): 2021-05-18 see ?sesameData and browseVignettes('sesameData') for documentation Setting options('download.file.method.GEOquery'='auto') Setting options('GEOquery.inmemory.gpl'=FALSE) snapshotDate(): 2021-05-18 see ?sesameData and browseVignettes('sesameData') for documentation Analyzing region chr22:17565612-17565675. For future calls to this function, perhaps specify a log file. Set the file name of the log file with the outLogFile argument. snapshotDate(): 2021-05-18 see ?sesameData and browseVignettes('sesameData') for documentation snapshotDate(): 2021-05-18 see ?sesameData and browseVignettes('sesameData') for documentation snapshotDate(): 2021-05-18 see ?sesameData and browseVignettes('sesameData') for documentation snapshotDate(): 2021-05-18 see ?sesameData and browseVignettes('sesameData') for documentation --- finished re-building ‘vin1_Introduction_to_coMethDMR_geneBasedPipeline.Rmd’

--- re-building ‘vin2_BiocParallel_for_coMethDMR_geneBasedPipeline 2.Rmd’ using rmarkdown Checking for cached SeSAMe data. snapshotDate(): 2021-05-18 snapshotDate(): 2021-05-18 see ?sesameData and browseVignettes('sesameData') for documentation snapshotDate(): 2021-05-18 see ?sesameData and browseVignettes('sesameData') for documentation Analyzing region chr22:30901532-30901886. Analyzing region chr22:39883190-39883347. Analyzing region chr22:30662799-30663041. Analyzing region chr22:43253521-43253559. For future calls to this function, perhaps specify a log file. Set the file name of the log file with the outLogFile argument. Error: processing vignette 'vin2_BiocParallel_for_coMethDMR_geneBasedPipeline 2.Rmd' failed with diagnostics: Failed to locate ‘weave’ output file ‘vin2_BiocParallel_for_coMethDMR_geneBasedPipeline 2.pdf’ or ‘vin2_BiocParallel_for_coMethDMR_geneBasedPipeline 2.html’ for vignette with name ‘vin2_BiocParallel_for_coMethDMR_geneBasedPipeline 2’ and engine ‘knitr::rmarkdown’. The following files exist in working directory ‘/Users/fernandaveitzman/Documents/GitHub/coMethDMR.Rcheck/vign_test/coMethDMR/vignettes’: ‘vin1_Introduction_to_coMethDMR_geneBasedPipeline 2.Rmd’ (18385 bytes), ‘vin1_Introduction_to_coMethDMR_geneBasedPipeline-2.R’ (7016 bytes), ‘vin1_Introduction_to_coMethDMR_geneBasedPipeline-2.html’ (861577 bytes), ‘vin1_Introduction_to_coMethDMR_geneBasedPipeline.R’ (7016 bytes), ‘vin1_Introduction_to_coMethDMR_geneBasedPipeline.Rmd’ (18385 bytes), ‘vin1_Introduction_to_coMethDMR_geneBasedPipeline.html’ (861577 bytes), ‘vin2_BiocParallel_for_coMethDMR_geneBasedPipeline 2.Rmd’ (10361 bytes), ‘vin2_BiocParallel_for_coMethDMR_geneBasedPipeline-2.R’ (3617 bytes), ‘vin2_BiocParallel_for_coMethDMR_geneBasedPipeline-2.html’ (768223 bytes), ‘vin2_BiocParallel_for_coMethDMR_geneBasedPipeline.Rmd’ (10361 bytes) --- failed re-building ‘vin2_BiocParallel_for_coMethDMR_geneBasedPipeline 2.Rmd’

--- re-building ‘vin2_BiocParallel_for_coMethDMR_geneBasedPipeline.Rmd’ using rmarkdown Checking for cached SeSAMe data. snapshotDate(): 2021-05-18 snapshotDate(): 2021-05-18 see ?sesameData and browseVignettes('sesameData') for documentation snapshotDate(): 2021-05-18 see ?sesameData and browseVignettes('sesameData') for documentation Analyzing region chr22:30901532-30901886. Analyzing region chr22:39883190-39883347. Analyzing region chr22:30662799-30663041. Analyzing region chr22:43253521-43253559. For future calls to this function, perhaps specify a log file. Set the file name of the log file with the outLogFile argument. --- finished re-building ‘vin2_BiocParallel_for_coMethDMR_geneBasedPipeline.Rmd’ SUMMARY: processing the following files failed: ‘vin1_Introduction_to_coMethDMR_geneBasedPipeline 2.Rmd’ ‘vin2_BiocParallel_for_coMethDMR_geneBasedPipeline 2.Rmd’ Error: Vignette re-building failed. Error: Duplicate vignette titles. Ensure that the %\VignetteIndexEntry lines in the vignette sources correspond to the vignette titles. Execution halted

checking package dependencies ... NOTE

Package suggested but not available for checking: ‘IlluminaHumanMethylationEPICanno.ilm10b4.hg19’

checking R code for possible problems ... NOTE

File ‘coMethDMR/R/zzz.R’: .onLoad calls: packageStartupMessage("Checking for cached SeSAMe data.") packageStartupMessage("Caching SeSAMe data for 450k/EPIC arrays.") See section ‘Good practice’ in '?.onAttach'. 0 errors ✓ | 3 warnings x | 2 notes xError: R CMD check found WARNINGsExecution halted Exited with status 1. On Mon, Apr 4, 2022 at 7:37 PM Tiago Chedraoui Silva < ***@***.***> wrote:

…

It was in the wrong branch. Now it is in the master On Mon, Apr 4, 2022, 7:13 PM Fernanda Veitzman ***@***.***> wrote: > I have just checked it, please find below the output: > > Error: .onLoad failed in loadNamespace() for 'coMethDMR', details: > call: tail(names(res[res$title == char, ]), 1) error: could not > find function "tail" Execution halted > 0 errors ✓ | 2 warnings x | 3 notes xError: R CMD check found > WARNINGsExecution halted > Exited with status 1. > > > > On Mon, Apr 4, 2022 at 6:08 PM Tiago Chedraoui Silva < > ***@***.***> wrote: > > > I sent the updates and ran check on my end. It passed for me. > > > > On Mon, Apr 4, 2022, 5:15 PM Fernanda Veitzman ***@***.***> > > wrote: > > > > > Hi Gabriel and Tiago, > > > Yes, sure. > > > Just let me know when it's ready and I will do it on my end. > > > Thank you. > > > > > > > > > On Mon, Apr 4, 2022 at 2:46 PM Gabriel J. Odom ***@***.***> > > > wrote: > > > > > > > Assigned #21 < #21 > > > > to > > > > @fveitz <https://github.com/fveitz>. > > > > > > > > — > > > > Reply to this email directly, view it on GitHub > > > > < > > #21 (comment) > > > >, > > > > or unsubscribe > > > > < > > > > > > https://github.com/notifications/unsubscribe-auth/ASCHHMUFC7B4QN63IODBLSLVDM2JBANCNFSM5SQNMCJQ > > > > > > > > . > > > > You are receiving this because you were assigned.Message ID: > > > > ***@***.***> > > > > > > > > > > — > > > Reply to this email directly, view it on GitHub > > > < > > > #21 (comment) > > >, > > > or unsubscribe > > > < > > > https://github.com/notifications/unsubscribe-auth/AABDQ6POKKMK257QQRSM5B3VDNLXBANCNFSM5SQNMCJQ > > > > > > . > > > You are receiving this because you were assigned.Message ID: > > > ***@***.***> > > > > > > > — > > Reply to this email directly, view it on GitHub > > < > #21 (comment) > >, > > or unsubscribe > > < > https://github.com/notifications/unsubscribe-auth/ASCHHMXLHKXDIKWBNSZSSGLVDNR7BANCNFSM5SQNMCJQ > > > > . > > You are receiving this because you were mentioned.Message ID: > > ***@***.***> > > > > — > Reply to this email directly, view it on GitHub > < #21 (comment) >, > or unsubscribe > < https://github.com/notifications/unsubscribe-auth/AABDQ6NHI3TKP4MTLNADESLVDNZSBANCNFSM5SQNMCJQ > > . > You are receiving this because you were assigned.Message ID: > ***@***.***> > — Reply to this email directly, view it on GitHub <#21 (comment)>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/ASCHHMRAY2HPDBIKKGJSFFLVDN4KFANCNFSM5SQNMCJQ> . You are receiving this because you were mentioned.Message ID: ***@***.***>

[gabrielodom]

Shoot. Let me take a look tomorrow.

[gabrielodom]

@fveitz, do you have a link to the build report?

[fveitz]

Hi @gabrielodom,
I have just pulled, installed, restarted and checked the package.
Please find bellow the results:

0 errors ✓ | 1 warning x | 4 notes xError: R CMD check found WARNINGs
Execution halted

Exited with status 1.

Warning in utils::tar(filepath, pkgname, compression = compression, compression_level = 9L, :
storing paths of more than 100 bytes is not portable:
‘coMethDMR/docs/articles/vin1_Introduction_to_coMethDMR_geneBasedPipeline_files/figure-html/unnamed-chunk-5-1.png’

W checking package subdirectories ...
Subdirectory 'man' contains invalid file names:
‘.AnnotateResults 3.Rd.icloud’ ‘.CloseBySingleRegion 2.Rd.icloud’
‘.CoMethAllRegions 2.Rd.icloud’ ‘.CoMethSingleRegion 2.Rd.icloud’
‘.CpGsInfoAllRegions 2.Rd.icloud’ ‘.CpGsInfoOneRegion 2.Rd.icloud’
‘.CreateOutputDF 2.Rd.icloud’ ‘.CreateParallelWorkers 2.Rd.icloud’
‘.CreateRdrop 2.Rd.icloud’ ‘.FindComethylatedRegions 2.Rd.icloud’
‘.GetCpGsInRegion 2.Rd.icloud’ ‘.GetResiduals 2.Rd.icloud’
‘.ImportSesameData 2.Rd.icloud’ ‘.MarkComethylatedCpGs 2.Rd.icloud’
‘.MarkMissing 2.Rd.icloud’ ‘.NameRegion 2.Rd.icloud’
‘.OrderCpGsByLocation 2.Rd.icloud’ ‘.RegionsToRanges 2.Rd.icloud’
‘.SplitCpGDFbyRegion 2.Rd.icloud’ ‘.WriteCloseByAllRegions
2.Rd.icloud’ ‘.betaMatrix_ex1 2.Rd.icloud’ ‘.betaMatrix_ex2
2.Rd.icloud’ ‘.betaMatrix_ex3 2.Rd.icloud’ ‘.betaMatrix_ex4
2.Rd.icloud’ ‘.betasChr22_df 2.Rd.icloud’ ‘.coMethDMR_setup
2.Rd.icloud’ ‘.lmmTest 2.Rd.icloud’ ‘.lmmTestAllRegions 2.Rd.icloud’
‘.pheno_df 3.Rd.icloud’
Please remove or rename the files.
See section ‘Package subdirectories’ in the ‘Writing R Extensions’
manual.

N checking package dependencies (10.7s)
Package suggested but not available for checking: ‘IlluminaHumanMethylationEPICanno.ilm10b4.hg19’

N checking for portable file names ...
Found the following non-portable file path:
coMethDMR/docs/articles/vin1_Introduction_to_coMethDMR_geneBasedPipeline_files/figure-html/unnamed-chunk-5-1.png

N checking top-level files
Non-standard files/directories found at top level:
‘_pkgdown.yaml’ ‘docs’

N checking R code for possible problems (49.5s)
File ‘coMethDMR/R/zzz.R’:
.onLoad calls:
packageStartupMessage("Checking for cached SeSAMe data.")
packageStartupMessage("Caching SeSAMe data for 450k/EPIC arrays.")

See section ‘Good practice’ in '?.onAttach'.