On Sun, Aug 9, 2020 at 6:57 AM Mikhail Dozmorov <mikhail.dozmo...@gmail.com> wrote:
> Thanks, Vincent. If I clone the Bioconductor version > from g...@git.bioconductor.org:packages/HiCcompare, it builds > without errors. The version from > https://github.com/dozmorovlab/HiCcompare.git, which supposed to be > identical, errors as before - rcmdcheck::rcmdcheck() throws the same > "supposed to be identical" but no -- I checked out the one you mention above, reproduced the error you report with R CMD *build* but note that the versions in DESCRIPTION are different, and, for example stvjc@stvjc-XPS-13-9300:~/BIOC_SOURCES/MIK/HiCcompare/R$ diff hic_compare.R ~/BIOC_SOURCES/HiCcompare/R/hic_compare.R 99c99 < A.min <- ceiling(mean(A_q10)) --- > A.min <- mean(A_q10) %>% ceiling() perhaps there is a branch in your lab repo that needs to be checked out? Error: processing vignette 'HiCcompare-vignette.Rmd' failed with diagnostics: > > non-conformable arrays > But the vignette builds using the "Knit" button. > > I still don't understand what is going on. The MD5 sums for files in both > repositories are identical, except some in .git folder. I'll use the > Bioconductor version and we don't need to dig more since this version > works. Still, very strange situation. > > Thanks again, > Mikhail > > On Sat, Aug 8, 2020 at 7:12 AM Vincent Carey <st...@channing.harvard.edu> > wrote: > >> Hi Mikhail -- I cannot reproduce your problem. I think I need more >> details as to how >> your error is triggered. Using rcmdcheck::rcmdcheck within R as shown in >> this transcript, >> on the built tar.gz from the current git checkout master branch, I have >> >> ── R CMD check results ────────────────────────────────── HiCcompare >> 1.11.0 ──── >> Duration: 3m 11.5s >> >> ❯ checking installed package size ... NOTE >> installed size is 6.2Mb >> sub-directories of 1Mb or more: >> data 5.6Mb >> >> ❯ checking R code for possible problems ... NOTE >> .adjust_pval : <anonymous>: no visible binding for global variable >> ‘p.adj’ >> .adjust_pval : <anonymous>: no visible binding for global variable >> ‘p.value’ >> .adjust_pval: no visible binding for global variable ‘p.value’ >> .adjust_pval: no visible binding for global variable ‘p.adj’ >> .calc.diff.thresh: no visible global function definition for ‘sd’ >> .calc.pval: no visible binding for global variable ‘D’ >> .calc.pval: no visible binding for global variable ‘p.value’ >> .calc.pval: no visible binding for global variable ‘p.adj’ >> .calc.pval: no visible binding for global variable ‘adj.M’ >> .calc.pval: no visible binding for global variable ‘fold.change’ >> .calc.pval: no visible binding for global variable ‘adj.IF2’ >> .calc.pval: no visible binding for global variable ‘adj.IF1’ >> .calc_z2: no visible global function definition for ‘sd’ >> .calc_z2: no visible binding for global variable ‘Z’ >> .calc_z2: no visible global function definition for ‘pnorm’ >> .calc_z2: no visible binding for global variable ‘p.value’ >> .loess.matrix: no visible binding for global variable ‘adj.IF1’ >> .loess.matrix: no visible binding for global variable ‘IF1’ >> .loess.matrix: no visible binding for global variable ‘adj.IF2’ >> .loess.matrix: no visible binding for global variable ‘IF2’ >> .loess.matrix: no visible binding for global variable ‘adj.M’ >> .loess.matrix: no visible binding for global variable ‘A’ >> .sim.mat: no visible global function definition for ‘head’ >> .split_cent: no visible binding for global variable >> ‘centromere_locations’ >> .split_cent: no visible binding for global variable ‘start1’ >> .split_cent: no visible binding for global variable ‘start2’ >> .split_cent: no visible binding for global variable ‘chr1’ >> .split_cent: no visible binding for global variable ‘chr2’ >> MA_norm: no visible binding for global variable ‘D’ >> MA_norm: no visible binding for global variable ‘M’ >> MA_norm: no visible binding for global variable ‘adj.IF1’ >> MA_norm: no visible binding for global variable ‘IF1’ >> MA_norm: no visible binding for global variable ‘adj.IF2’ >> MA_norm: no visible binding for global variable ‘IF2’ >> MA_norm: no visible binding for global variable ‘adj.M’ >> cooler2sparse: no visible binding for global variable ‘chr1’ >> cooler2sparse: no visible binding for global variable ‘chr2’ >> cooler2sparse: no visible binding for global variable ‘IF’ >> create.hic.table: no visible binding for global variable ‘D’ >> create.hic.table: no visible binding for global variable ‘region2’ >> create.hic.table: no visible binding for global variable ‘region1’ >> create.hic.table: no visible binding for global variable ‘IF2’ >> create.hic.table: no visible binding for global variable ‘M’ >> create.hic.table: no visible binding for global variable ‘IF1’ >> create.hic.table: no visible binding for global variable ‘i’ >> create.hic.table: no visible binding for global variable ‘j’ >> filter_params: no visible binding for global variable ‘M’ >> filter_params: no visible binding for global variable ‘IF1’ >> filter_params: no visible binding for global variable ‘IF2’ >> filter_params: no visible global function definition for ‘axis’ >> full2sparse: no visible binding for global variable ‘IF’ >> hic_compare : <anonymous>: no visible binding for global variable >> ‘p.adj’ >> hic_simulate: no visible binding for global variable ‘bias.slope’ >> hic_simulate: no visible global function definition for ‘na.omit’ >> hicpro2bedpe: no visible binding for global variable ‘chr1’ >> hicpro2bedpe: no visible binding for global variable ‘chr2’ >> manhattan_plot: no visible binding for global variable ‘bp’ >> manhattan_plot: no visible binding for global variable ‘count’ >> sim.other.methods: no visible binding for global variable ‘adj.IF1’ >> sim.other.methods: no visible binding for global variable ‘IF1’ >> sim.other.methods: no visible binding for global variable ‘adj.IF2’ >> sim.other.methods: no visible binding for global variable ‘IF2’ >> sim.other.methods: no visible binding for global variable ‘adj.M’ >> sim.other.methods: no visible binding for global variable ‘M’ >> sim.other.methods: no visible global function definition for ‘na.omit’ >> sim_matrix: no visible binding for global variable ‘bias.slope’ >> total_sum: no visible binding for global variable ‘IF2’ >> total_sum: no visible binding for global variable ‘M’ >> total_sum: no visible binding for global variable ‘IF1’ >> total_sum: no visible binding for global variable ‘chr1’ >> volcano: no visible binding for global variable ‘A’ >> volcano: no visible binding for global variable ‘adj.IF1’ >> volcano: no visible binding for global variable ‘adj.IF2’ >> volcano: no visible binding for global variable ‘p.value’ >> volcano: no visible binding for global variable ‘D’ >> Undefined global functions or variables: >> A D IF IF1 IF2 M Z adj.IF1 adj.IF2 adj.M axis bias.slope bp >> centromere_locations chr1 chr2 count fold.change head i j na.omit >> p.adj p.value pnorm region1 region2 sd start1 start2 >> Consider adding >> importFrom("graphics", "axis") >> importFrom("stats", "D", "na.omit", "pnorm", "sd") >> importFrom("utils", "head") >> to your NAMESPACE file. >> >> 0 errors ✔ | 0 warnings ✔ | 2 notes ✖ >> > sessionInfo() >> R version 4.0.2 Patched (2020-07-19 r78892) >> Platform: x86_64-pc-linux-gnu (64-bit) >> Running under: Ubuntu 20.04 LTS (fossa-melisa X20) >> >> Matrix products: default >> BLAS: /home/stvjc/R-4-0-dist/lib/R/lib/libRblas.so >> LAPACK: /home/stvjc/R-4-0-dist/lib/R/lib/libRlapack.so >> >> locale: >> [1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C >> [3] LC_TIME=en_US.UTF-8 LC_COLLATE=en_US.UTF-8 >> [5] LC_MONETARY=en_US.UTF-8 LC_MESSAGES=en_US.UTF-8 >> [7] LC_PAPER=en_US.UTF-8 LC_NAME=C >> [9] LC_ADDRESS=C LC_TELEPHONE=C >> [11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C >> >> attached base packages: >> [1] stats graphics grDevices utils datasets methods base >> >> other attached packages: >> [1] rcmdcheck_1.3.3 >> >> loaded via a namespace (and not attached): >> [1] ps_1.3.3 fansi_0.4.1 prettyunits_1.1.1 withr_2.2.0 >> >> [5] digest_0.6.25 crayon_1.3.4 rprojroot_1.3-2 >> assertthat_0.2.1 >> [9] R6_2.4.1 backports_1.1.8 cli_2.0.2 callr_3.4.3 >> >> [13] desc_1.2.0 tools_4.0.2 glue_1.4.1 compiler_4.0.2 >> >> [17] processx_3.4.3 xopen_1.0.0 pkgbuild_1.1.0 >> > >> >> On Fri, Aug 7, 2020 at 7:08 PM Mikhail Dozmorov < >> mikhail.dozmo...@gmail.com> wrote: >> >>> Dear Bioconductor team, >>> >>> I am trying to update a package we developed, HiCcompare. >>> https://bioconductor.org/packages/HiCcompare/. The package has been >>> successfully submitted previously. However, now `R CMD check` throws an >>> error: >>> E> Quitting from lines 426-427 (HiCcompare-vignette.Rmd) >>> E> Error: processing vignette 'HiCcompare-vignette.Rmd' failed with >>> diagnostics: >>> E> non-conformable arrays >>> E> --- failed re-building ‘HiCcompare-vignette.Rmd’ >>> >>> Yet, If I knit the vignette manually, it builds. If I execute the code >>> manually, it works. If I install the package from Bioconductor, it also >>> works. >>> >>> I'm working with this package using >>> bioconductor/bioconductor_docker:devel. >>> But the strange behavior - vignette knits manually but fails in CMD >>> check - >>> persists both in Docker container and on local R installation. >>> >>> Please advise, where to troubleshoot next. >>> Thanks, >>> Mikhail >>> >>> --- >>> Mikhail Dozmorov, Ph.D., Blick scholar >>> Associate Professor, Department of Biostatistics >>> Affiliate, Department of Pathology >>> Virginia Commonwealth University >>> OCS #738, 830 E. Main St, RVA, 23298 >>> E-mail: mikhail.dozmo...@vcuhealth.org >>> Phone: 804-827-2055 >>> https://medschool.vcu.edu/expertise/detail.html?id=mdozmorov >>> >>> [[alternative HTML version deleted]] >>> >>> _______________________________________________ >>> Bioc-devel@r-project.org mailing list >>> https://stat.ethz.ch/mailman/listinfo/bioc-devel >>> >> >> The information in this e-mail is intended only for the person to whom it >> is >> addressed. If you believe this e-mail was sent to you in error and the >> e-mail >> contains patient information, please contact the Partners Compliance HelpLine >> at >> http://www.partners.org/complianceline . If the e-mail was sent to you >> in error >> but does not contain patient information, please contact the sender and >> properly >> dispose of the e-mail. > > -- The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline <http://www.partners.org/complianceline> . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail. [[alternative HTML version deleted]] _______________________________________________ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel