[Bioc-devel] non-conformable arrays
Vincent Carey
@tvjc @end|ng |rom ch@nn|ng@h@rv@rd@edu
Sat Aug 8 13:12:07 CEST 2020
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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