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 ?
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]]