Re: [Bioc-devel] cannot reproduce the build error with InTAD package
It looks like you are creating a MultiAssayExperiment in your vignette. Numerous Bioconductor packages relying on MultiAssayExperiment infrastructure started failing a few days ago with the release of version 1.17.3, but I don't see the breaking change explained in the News file. ___ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel
Re: [Bioc-devel] Recent change in MultiAssayExperiment for inferred MAE-level colData
This also happens to ClassifyR. ___ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel
[Bioc-devel] Fwd: Bioconductor package EnMCB
Dear bioconductor team, I am working on our package EnMCB, which recently have some problems on developing branch, I fixed most of the errors but our package still has a warning in check as follows: * checking PDF version of manual ... WARNING LaTeX errors when creating PDF version. This typically indicates Rd problems. LaTeX errors when creating PDF version. This typically indicates Rd problems. LaTeX errors found: ! Package inputenc Error: Unicode character ≤ (U+2264) (inputenc)not set up for use with LaTeX. See the inputenc package documentation for explanation. Type H for immediate help. ! Package inputenc Error: Unicode character ≤ (U+2264) (inputenc)not set up for use with LaTeX. See the inputenc package documentation for explanation. Type H for immediate help. * checking PDF version of manual without hyperrefs or index ... ERROR * DONE I checked our package on the local computer and looks fine. I can not find out which character causes this problem. Could you please help me to fix this issue? Thanks in advance. Merry Christmas! Best Regards, Xin Yu Ph.D. student of Biomedical Informatics College of Bioinformatics - Huazhong Agricultural University whirl...@gmail.com yu...@webmail.hzau.edu.cn tel: (+86) 186-5313-5769 xin wwa 于2020年12月23日周三 下午8:26写道： > Dear Lori, > > Thank you for your email, we currently are working on upgrading our > package. > It should be work fine after our update. > > Best regards, > Xin Yu > Ph.D. student of Biomedical Informatics > College of Bioinformatics - Huazhong Agricultural University > whirl...@gmail.com > yu...@webmail.hzau.edu.cn > tel: (+86) 186-5313-5769 > > > Kern, Lori 于2020年12月23日周三 下午8:20写道： > >> Hello Package Maintainer, >> >> The Bioconductor Team would like to notify you that your package is >> currently >> failing on the devel 3.13 version of Bioconductor, and has been for an >> extended >> period of time. Please fix your package to R CMD build and R CMD check >> cleanly >> immediately to avoid deprecation of your package. While devel is a place >> to >> experiment with new features, we expect packages to build and check >> cleanly in a >> reasonable time period and not stay broken for any extended period of >> time. If >> you are having trouble or have any further questions please do not >> hesitate to >> reach out to the developers mailing list at bioc-devel@r-project.org. >> The package has been failing consistently since 12/04/20 >> >> bioconductor.org/checkResults/devel/bioc-LATEST/EnMCB >> >> >> Lori Shepherd >> >> Bioconductor Core Team >> >> Roswell Park Comprehensive Cancer Center >> >> Department of Biostatistics & Bioinformatics >> >> Elm & Carlton Streets >> >> Buffalo, New York 14263 >> >> This email message may contain legally privileged and/or confidential >> information. If you are not the intended recipient(s), or the employee or >> agent responsible for the delivery of this message to the intended >> recipient(s), you are hereby notified that any disclosure, copying, >> distribution, or use of this email message is prohibited. If you have >> received this message in error, please notify the sender immediately by >> e-mail and delete this email message from your computer. Thank you. > > [[alternative HTML version deleted]] ___ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel
Re: [Bioc-devel] cannot reproduce the build error with InTAD package
Hi Konstantin,
It seems this is a new issue. Please give the devel build machine one more
cycle and we'll see if the issue persists.
Did you try to build it using the command in the build machine log (although I
doubt it'll change the end result of successfully building on the
bioconductor_docker:devel image) ?
R CMD build --keep-empty-dirs --no-resave-data InTAD
Best,
Nitesh
On 12/28/20, 2:07 AM, "Bioc-devel on behalf of Konstantin Okonechnikov"
wrote:
Hi!
I got a note about failing for InTAD package only in Bioc-devel version:
http://bioconductor.org/checkResults/devel/bioc-LATEST/InTAD/machv2-buildsrc.html
Notably, there were no changes to the package before this error started
occurring thus I suppose it might be connected to some updates in other
packages.
To reproduce the issue I installed the latest available R-devel version and
also switched to bioconductor-devel. Installing the package worked OK.
Error message from report was the following:
Quitting from lines 93-94 (InTAD.Rmd)
Error: processing vignette 'InTAD.Rmd' failed with diagnostics:
missing value where TRUE/FALSE needed
--- failed re-building ‘InTAD.Rmd’
The problem seems to be occurring in creating the object (
https://github.com/kokonech/InTAD/blob/master/vignettes/InTAD.Rmd
):
*inTadSig <- newSigInTAD(enhSel, enhSelGR, rpkmCountsSel, txsSel,mbAnnData)*
However, I did not observe any issues in package installation. Moreover, I
managed to build the vignette without problems simply running the following
command from latest source:
*rmarkdown::render('InTAD/vignettes/InTAD.Rmd') *
Any suggestions how I could reproduce and fix this error? Below I also
included my sessionInfo()
Best regards,
Konstantin
*R Under development (unstable) (2020-12-26 r79698)Platform:
x86_64-pc-linux-gnu (64-bit)Running under: openSUSE Leap 42.3Matrix
products: defaultBLAS:
/home/okonechn/B080/okonechn/tools/R-devel/lib/libRblas.soLAPACK:
/home/okonechn/B080/okonechn/tools/R-devel/lib/libRlapack.solocale:[1]
Cattached base packages:[1] parallel stats4stats graphics
grDevices utils datasets[8] methods baseother attached packages: [1]
BiocStyle_2.19.1InTAD_1.11.0 [3] MultiAssayExperiment_1.17.2
SummarizedExperiment_1.21.1 [5] Biobase_2.51.0
MatrixGenerics_1.3.0 [7] matrixStats_0.57.0
GenomicRanges_1.43.1 [9] GenomeInfoDb_1.27.3 IRanges_2.25.6[11]
S4Vectors_0.29.6BiocGenerics_0.37.0loaded via a namespace (and
not attached): [1] tidyr_1.1.2 splines_4.1.0
carData_3.0-4 [4] BiocManager_1.30.10 GenomeInfoDbData_1.2.4
cellranger_1.1.0 [7] Rsamtools_2.7.0 yaml_2.2.1
pillar_1.4.7[10] backports_1.2.1 lattice_0.20-41
glue_1.4.2[13] digest_0.6.27ggsignif_0.6.0
XVector_0.31.1[16] qvalue_2.23.0colorspace_2.0-0
htmltools_0.5.0[19] Matrix_1.3-0 plyr_1.8.6
XML_3.99-0.5[22] pkgconfig_2.0.3 broom_0.7.3
haven_2.3.1[25] bookdown_0.21zlibbioc_1.37.0
purrr_0.3.4[28] scales_1.1.1 openxlsx_4.2.3
rio_0.5.16[31] BiocParallel_1.25.2 tibble_3.0.4
farver_2.0.3[34] generics_0.1.0 car_3.0-10
ggplot2_3.3.2[37] ellipsis_0.3.1 ggpubr_0.4.0
magrittr_2.0.1[40] crayon_1.3.4 readxl_1.3.1
mclust_5.4.7[43] evaluate_0.14rstatix_0.6.0
forcats_0.5.0[46] foreign_0.8-81 tools_4.1.0
data.table_1.13.4[49] hms_0.5.3BiocIO_1.1.2
lifecycle_0.2.0[52] stringr_1.4.0munsell_0.5.0
zip_2.1.1[55] DelayedArray_0.17.7 Biostrings_2.59.2
compiler_4.1.0[58] rlang_0.4.9 grid_4.1.0
RCurl_1.98-1.2[61] rjson_0.2.20 labeling_0.4.2
rmarkdown_2.6[64] bitops_1.0-6 restfulr_0.0.13
gtable_0.3.0[67] abind_1.4-5 curl_4.3
reshape2_1.4.4[70] R6_2.5.0 GenomicAlignments_1.27.2
knitr_1.30[73] dplyr_1.0.2 rtracklayer_1.51.2
stringi_1.5.3[76] Rcpp_1.0.5 vctrs_0.3.6
xfun_0.19[79] tidyselect_1.1.0*
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[Rd] Suppress conflict messages when mask.ok
I was very happy to see the new mask.ok option. It works very well when
conflicts.policy is "strict":
---
options(conflicts.policy="strict")
library(igraph, exclude="decompose", mask.ok=c("spectrum","union"))
#> [No messages]
---
However, if no conflicts.policy has been set, the masked objects are loudly
reported, even if they are specified with mask.ok:
---
library(igraph, exclude="decompose", mask.ok=c("spectrum","union"))
#>
#> Attaching package: 'igraph'
#> The following object is masked from 'package:stats':
#>
#> spectrum
#> The following object is masked from 'package:base':
#>
#> union
---
It seems that if I specify mask.ok, that particular masking is expected and
should NOT be reported, regardless of what the conflicts.policy is. It
would be very useful for many users who are not ready to switch over to a
strict conflicts.policy, to nevertheless be able to suppress messages about
expected conflicts using mask.ok and thus only get messages when unexpected
masking occurs.
Best,
Magnus
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Re: [Rd] installing from source
Kevin Ushey pointed out to me privately that he submitted a bug
report and a patch for this about a month ago, which Kurt Hornik put in
R-devel (c79477):
https://bugs.r-project.org/bugzilla/show_bug.cgi?id=17973
On 12/28/20 4:35 AM, Martin Maechler wrote:
Ben Bolker
on Sun, 27 Dec 2020 15:02:47 -0500 writes:
> There is a recurring issue with installing from source into paths
> that contain single quotes/apostrophes. "Why would anyone do that??" is
> certainly a legitimate response to such a problem, but I would also say
> this constitutes a legitimate bug. Would replacing both single-quotes
> below with \\' solve the problem?
Here, I'm mostly among the "Why would anyone do that??" people,
but I agree that it's worth some effort to try fixing this.
To your question above: Why don't you create a repr.ex. (we'd
want anyway for R-bugzilla) and *see* if your proposition solves
it - or did I misinterpret the Q?
> I'm happy to post this (with a patch if my fix seems appropriate) on
> r-bugzilla.
> cheers
> Ben Bolker
> line 1672 of src/library/tools/R/install.R :
> cmd <- paste0("tools:::.test_load_package('", pkg_name, "', ",
> quote_path(lib), ")")
>
https://github.com/wch/r-source/blob/2eade649c80725352256f16509f9ff6919fd079c/src/library/tools/R/install.R#L1672
>
https://stackoverflow.com/questions/15129888/r-cmd-install-error-unexpected-symbol-in-test-load-package-function
>
https://stackoverflow.com/questions/65462881/cannot-download-packages-from-github-from-unexpected-symbol
> __
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Re: [Rd] .Fortran to .Call
Roger, Over the years I have converted many of the .C calls in the survival package to .Call. As others have said, the big advantage is memory footprint. I did it because there are a few users who call survfit or coxph with really large data sets, and not copying the data can be the difference between success and failure (run out of memory). Like you, my experience has been that if there is enough memory, then the time required for .C or .Fortran to make the data copy is minimal. Don't make the change in order to gain compute speed. The downside to .Call is that R then makes the (dangerous) assumption that you know what you are doing. That is, vectors/matrices that are passed in to the function will NOT have new data values written into them, unless you have taken the necessary steps. Breaking the promise can lead to program failures that are very hard to track down. -- Terry M Therneau, PhD Department of Health Science Research Mayo Clinic thern...@mayo.edu "TERR-ree THUR-noh" [[alternative HTML version deleted]] __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel
[Bioc-devel] cannot reproduce the build error with InTAD package
Hi!
I got a note about failing for InTAD package only in Bioc-devel version:
http://bioconductor.org/checkResults/devel/bioc-LATEST/InTAD/machv2-buildsrc.html
Notably, there were no changes to the package before this error started
occurring thus I suppose it might be connected to some updates in other
packages.
To reproduce the issue I installed the latest available R-devel version and
also switched to bioconductor-devel. Installing the package worked OK.
Error message from report was the following:
Quitting from lines 93-94 (InTAD.Rmd)
Error: processing vignette 'InTAD.Rmd' failed with diagnostics:
missing value where TRUE/FALSE needed
--- failed re-building ‘InTAD.Rmd’
The problem seems to be occurring in creating the object (
https://github.com/kokonech/InTAD/blob/master/vignettes/InTAD.Rmd
):
*inTadSig <- newSigInTAD(enhSel, enhSelGR, rpkmCountsSel, txsSel,mbAnnData)*
However, I did not observe any issues in package installation. Moreover, I
managed to build the vignette without problems simply running the following
command from latest source:
*rmarkdown::render('InTAD/vignettes/InTAD.Rmd') *
Any suggestions how I could reproduce and fix this error? Below I also
included my sessionInfo()
Best regards,
Konstantin
*R Under development (unstable) (2020-12-26 r79698)Platform:
x86_64-pc-linux-gnu (64-bit)Running under: openSUSE Leap 42.3Matrix
products: defaultBLAS:
/home/okonechn/B080/okonechn/tools/R-devel/lib/libRblas.soLAPACK:
/home/okonechn/B080/okonechn/tools/R-devel/lib/libRlapack.solocale:[1]
Cattached base packages:[1] parallel stats4stats graphics
grDevices utils datasets[8] methods baseother attached packages: [1]
BiocStyle_2.19.1InTAD_1.11.0 [3] MultiAssayExperiment_1.17.2
SummarizedExperiment_1.21.1 [5] Biobase_2.51.0
MatrixGenerics_1.3.0 [7] matrixStats_0.57.0
GenomicRanges_1.43.1 [9] GenomeInfoDb_1.27.3 IRanges_2.25.6[11]
S4Vectors_0.29.6BiocGenerics_0.37.0loaded via a namespace (and
not attached): [1] tidyr_1.1.2 splines_4.1.0
carData_3.0-4 [4] BiocManager_1.30.10 GenomeInfoDbData_1.2.4
cellranger_1.1.0 [7] Rsamtools_2.7.0 yaml_2.2.1
pillar_1.4.7[10] backports_1.2.1 lattice_0.20-41
glue_1.4.2[13] digest_0.6.27ggsignif_0.6.0
XVector_0.31.1[16] qvalue_2.23.0colorspace_2.0-0
htmltools_0.5.0[19] Matrix_1.3-0 plyr_1.8.6
XML_3.99-0.5[22] pkgconfig_2.0.3 broom_0.7.3
haven_2.3.1[25] bookdown_0.21zlibbioc_1.37.0
purrr_0.3.4[28] scales_1.1.1 openxlsx_4.2.3
rio_0.5.16[31] BiocParallel_1.25.2 tibble_3.0.4
farver_2.0.3[34] generics_0.1.0 car_3.0-10
ggplot2_3.3.2[37] ellipsis_0.3.1 ggpubr_0.4.0
magrittr_2.0.1[40] crayon_1.3.4 readxl_1.3.1
mclust_5.4.7[43] evaluate_0.14rstatix_0.6.0
forcats_0.5.0[46] foreign_0.8-81 tools_4.1.0
data.table_1.13.4[49] hms_0.5.3BiocIO_1.1.2
lifecycle_0.2.0[52] stringr_1.4.0munsell_0.5.0
zip_2.1.1[55] DelayedArray_0.17.7 Biostrings_2.59.2
compiler_4.1.0[58] rlang_0.4.9 grid_4.1.0
RCurl_1.98-1.2[61] rjson_0.2.20 labeling_0.4.2
rmarkdown_2.6[64] bitops_1.0-6 restfulr_0.0.13
gtable_0.3.0[67] abind_1.4-5 curl_4.3
reshape2_1.4.4[70] R6_2.5.0 GenomicAlignments_1.27.2
knitr_1.30[73] dplyr_1.0.2 rtracklayer_1.51.2
stringi_1.5.3[76] Rcpp_1.0.5 vctrs_0.3.6
xfun_0.19[79] tidyselect_1.1.0*
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Re: [Rd] installing from source
> Ben Bolker
> on Sun, 27 Dec 2020 15:02:47 -0500 writes:
> There is a recurring issue with installing from source into paths
> that contain single quotes/apostrophes. "Why would anyone do that??" is
> certainly a legitimate response to such a problem, but I would also say
> this constitutes a legitimate bug. Would replacing both single-quotes
> below with \\' solve the problem?
Here, I'm mostly among the "Why would anyone do that??" people,
but I agree that it's worth some effort to try fixing this.
To your question above: Why don't you create a repr.ex. (we'd
want anyway for R-bugzilla) and *see* if your proposition solves
it - or did I misinterpret the Q?
> I'm happy to post this (with a patch if my fix seems appropriate) on
> r-bugzilla.
> cheers
> Ben Bolker
> line 1672 of src/library/tools/R/install.R :
> cmd <- paste0("tools:::.test_load_package('", pkg_name, "', ",
> quote_path(lib), ")")
>
https://github.com/wch/r-source/blob/2eade649c80725352256f16509f9ff6919fd079c/src/library/tools/R/install.R#L1672
>
https://stackoverflow.com/questions/15129888/r-cmd-install-error-unexpected-symbol-in-test-load-package-function
>
https://stackoverflow.com/questions/65462881/cannot-download-packages-from-github-from-unexpected-symbol
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[Bioc-devel] Recent change in MultiAssayExperiment for inferred MAE-level colData
Hello Marcel, Thanks to you for your very useful MultiAssayExperiment package, it has provided a very useful framework that I have made use of in my multi-omic package padma. I've noticed that padma has started breaking in devel due to a recent change in MultiAssayExperiment (v1.17.3, which is also currently not building on devel) that appears to be linked to a fix for issue #287 (https://github.com/waldronlab/MultiAssayExperiment/issues/287) about inferring MAE-level colData. The problem in padma seems to be in my vignette when an error message of "No matching identifiers found" is returned while subsetting a MultiAssayExperiment object. I'm guessing it should be an easy fix for me in my vignette/example code, but I first wanted to make sure that you're planning on keeping this inference of MAE-level colData in future versions of MultiAssayExperiment or whether this is still somewhat in flux. Thanks again, and wishing you happy holidays! Andrea [[alternative HTML version deleted]] ___ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel
