Message-ID: <CAANT7+Xh2-hX06+-dJGwkuM3yhZgN03GP+5PUq0JEh3Vi0S0Ag@mail.gmail.com>
Date: 2020-08-09T11:10:12Z
From: Vincent Carey
Subject: [Bioc-devel] non-conformable arrays
In-Reply-To: <CAAyWZnC0qpC38nr-E3XkD73f3KD9DThZ4iGkU=nM_qcTOJjTvw@mail.gmail.com>
On Sun, Aug 9, 2020 at 6:57 AM Mikhail Dozmorov <mikhail.dozmorov at gmail.com>
wrote:
> Thanks, Vincent. If I clone the Bioconductor version
> from git at 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 at 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 at 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 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
>>>
>>> [[alternative HTML version deleted]]
>>>
>>> _______________________________________________
>>> Bioc-devel at r-project.org mailing list
>>> https://stat.ethz.ch/mailman/listinfo/bioc-devel
>>>
>>
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