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 ...{{dropped:18}} _______________________________________________ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel