[Bioc-devel] non-conformable arrays

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.dozmorov at 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.dozmorov at vcuhealth.org
Phone: 804-827-2055
https://medschool.vcu.edu/expertise/detail.html?id=mdozmorov

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