[Bioc-devel] non-conformable arrays
Mikhail Dozmorov
m|kh@||@dozmorov @end|ng |rom gm@||@com
Sun Aug 9 14:50:40 CEST 2020
I see it now and didn't catch because ran md5sum on the same folder. Not
sure how the two repositories diverged. Will synchronize back, that should
solve the problem.
Thank you.
Mikhail
On Sun, Aug 9, 2020 at 7:10 AM Vincent Carey <stvjc using channing.harvard.edu>
wrote:
>
>
> 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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