[Bioc-devel] non-conformable arrays

[Vincent Carey]

On Sun, Aug 9, 2020 at 6:57 AM Mikhail Dozmorov <mikhail.dozmorov using gmail.com>
wrote:

> Thanks, Vincent. If I clone the Bioconductor version
> from git using 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 using 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 <stvjc using 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.dozmorov using 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 using vcuhealth.org
>>> Phone: 804-827-2055
>>> https://medschool.vcu.edu/expertise/detail.html?id=mdozmorov
>>>
>>>         [[alternative HTML version deleted]]
>>>
>>> _______________________________________________
>>> Bioc-devel using r-project.org mailing list
>>> https://stat.ethz.ch/mailman/listinfo/bioc-devel
>>>
>>
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