Closed gladkia closed 1 year ago
Hi @gladkia
Thanks for submitting your package. We are taking a quick look at it and you will hear back from us soon.
The DESCRIPTION file for this package is:
Type: Package
Package: gDR
Title: Umbrella package for R packages in the gDR suite
Version: 0.99.0
Date: 2023-03-23
Authors@R: c(
person("Support", "gDR", , "gdr-support-d@gene.com", role = "cre",
comment = c(ORCID = "0009-0006-9310-1135")),
person("Allison", "Vuong", , "vuong.allison@gene.com", role = "aut"),
person("Bartosz", "Czech", role = "aut"),
person("Arkadiusz", "Gladki", role = "aut"),
person("Marc", "Hafner", role = "aut"),
person("Dariusz", "Scigocki", role = "aut"),
person("Sergiu", "Mocanu", role = "aut")
)
Description: Package is a part of the gDR suite. It provides info about processing functions
and utilities from individual gDR packages. The vignette walks through
the full processing pipeline for drug response analyses that the gDR suite offers.
License: file LICENSE
Depends:
R (>= 4.2),
gDRcore (>= 0.99.0),
gDRimport (>= 0.99.0),
gDRutils (>= 0.99.0)
Suggests:
BumpyMatrix,
futile.logger,
gDRstyle (>= 0.99.0),
gDRtestData (>= 0.99.0),
kableExtra,
knitr,
markdown,
purrr,
rmarkdown,
SummarizedExperiment,
testthat,
yaml
VignetteBuilder:
knitr
biocViews: Software, DataImport
ByteCompile: TRUE
DeploySubPath: gDR
Encoding: UTF-8
LazyLoad: yes
RoxygenNote: 7.2.3
SwitchrLibrary: gDR
--- re-building ‘gDR.Rmd’ using knitr
Quitting from lines 95-98 (gDR.Rmd)
Error: processing vignette 'gDR.Rmd' failed with diagnostics:
'length = 3840' in coercion to 'logical(1)'
--- failed re-building ‘gDR.Rmd’
@vjcitn thanks - we will merge the bugfix soon (https://github.com/gdrplatform/gDRcore/pull/62).
@vjcitn fixed.
Hi @vjcitn and @lshep,
I would like to push the latest changes to git@git.bioconductor.org:packages/gDR.git
but I'm getting:
gladkia@gladkia-UHMD6M /tmp % git clone git@git.bioconductor.org:packages/gDR.git
Cloning into 'gDR'...
FATAL: R any packages/gDR gladkia DENIED by fallthru
(or you mis-spelled the reponame)
fatal: Could not read from remote repository.
Please make sure you have the correct access rights
and the repository exists.
I see the same issue for other packages, submitted as candidates for the 3.17 release, on which gDR depends (gDRcore, gDRutils, gDRimport, gDRtestData). How to solve it?
Thanks in advance for your help!
Best, Arek
I don't think we are using git.bioconductor.org yet ... the package is not far enough along. we are working from your github. And finding
* checking dependencies in R code ... WARNING
'loadNamespace' or 'requireNamespace' call not declared from: ‘gDRinternalData’
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... OK
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking line endings in C/C++/Fortran sources/headers ... OK
* checking compiled code ... OK
* checking installed files from 'inst/doc' ... OK
* checking files in 'vignettes' ... OK
* checking examples ... ERROR
Running examples in 'gDRcore-Ex.R' failed
The error most likely occurred in:
> ### Name: convert_mae_to_raw_data
> ### Title: Transform mae into raw data
> ### Aliases: convert_mae_to_raw_data
>
> ### ** Examples
>
> mae <- get_synthetic_data("finalMAE_small.RDS")
Error in get_synthetic_data("finalMAE_small.RDS") :
could not find function "get_synthetic_data"
Execution halted
Please sync all your packages to a consistent state in your github and ensure that they will pass check.
building gDR fails
* checking for file 'gDR/DESCRIPTION' ... OK
* preparing 'gDR':
* checking DESCRIPTION meta-information ... OK
* installing the package to build vignettes
* creating vignettes ... ERROR
--- re-building ‘gDR.Rmd’ using knitr
Quitting from lines 113-121 (gDR.Rmd)
Error: processing vignette 'gDR.Rmd' failed with diagnostics:
subscript contains invalid names
--- failed re-building ‘gDR.Rmd’
SUMMARY: processing the following file failed:
‘gDR.Rmd’
sessionInfo()
R Under development (unstable) (2023-03-18 r84003)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Ubuntu 20.04.6 LTS
Matrix products: default
BLAS: /home/stvjc/R-43dev-dist/lib/R/lib/libRblas.so
LAPACK: /home/stvjc/R-43dev-dist/lib/R/lib/libRlapack.so; LAPACK version 3.11.0
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
time zone: America/New_York
tzcode source: system (glibc)
attached base packages:
[1] stats graphics grDevices utils datasets methods base
other attached packages:
[1] gDR_0.99.3 gDRutils_0.99.4 gDRimport_0.99.3 gDRcore_0.99.3
[5] rmarkdown_2.21
loaded via a namespace (and not attached):
[1] Matrix_1.5-4 compiler_4.3.0
[3] SummarizedExperiment_1.29.1 Biobase_2.59.0
[5] GenomicRanges_1.51.4 bitops_1.0-7
[7] IRanges_2.33.1 fastmap_1.1.1
[9] lattice_0.21-8 XVector_0.39.0
[11] GenomeInfoDb_1.35.16 knitr_1.42
[13] BiocGenerics_0.45.3 backports_1.4.1
[15] DelayedArray_0.25.0 checkmate_2.1.0
[17] tibble_3.2.1 MatrixGenerics_1.11.1
[19] GenomeInfoDbData_1.2.10 pillar_1.9.0
[21] rlang_1.1.0 utf8_1.2.3
[23] xfun_0.38 cli_3.6.1
[25] magrittr_2.0.3 zlibbioc_1.45.0
[27] grid_4.3.0 digest_0.6.31
[29] lifecycle_1.0.3 S4Vectors_0.37.5
[31] vctrs_0.6.1 startup_0.20.0
[33] evaluate_0.20 glue_1.6.2
[35] data.table_1.14.8 stats4_4.3.0
[37] RCurl_1.98-1.12 fansi_1.0.4
[39] matrixStats_0.63.0 tools_4.3.0
[41] pkgconfig_2.0.3 htmltools_0.5.5
I am going to pass the pre-check so that the build system reports are directly addressible by you. I would not begin reviewing until you get to a WARNINGS state.
@vjcitn, thanks! Can you please give me some hints on how to trigger the build system reports?
@vjcitn, FYI, the error in the gDR vignette has just been fixed.
A reviewer has been assigned to your package. Learn what to expect during the review process.
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Dear Package contributor,
This is the automated single package builder at bioconductor.org.
Your package has been built on Linux, Mac, and Windows.
On one or more platforms, the build results were: "ERROR, skipped". This may mean there is a problem with the package that you need to fix. Or it may mean that there is a problem with the build system itself.
Please see the build report for more details. This link will be active for 21 days.
Remember: if you submitted your package after July 7th, 2020,
when making changes to your repository push to
git@git.bioconductor.org:packages/gDR
to trigger a new build.
A quick tutorial for setting up remotes and pushing to upstream can be found here.
td <- get_test_data()
td$m_file
[1] “/home/stvjc/R/x86_64-pc-linux-gnu-library/4.3/gDRimport/extdata/data1/manifest.xlsx”
td$t_files
[1] “/home/stvjc/R/x86_64-pc-linux-gnu-library/4.3/gDRimport/extdata/data1/Template_7daytreated.xlsx” [2] “/home/stvjc/R/x86_64-pc-linux-gnu-library/4.3/gDRimport/extdata/data1/Template_Untreated.xlsx”
This is quite unpleasant, in the vignette. You should define an object class that manages the paths, with methods that can use them. You don't have to use S4 but it is recommended.
td <- get_test_data() td$m_file [1] “/home/stvjc/R/x86_64-pc-linux-gnu-library/4.3/gDRimport/extdata/data1/manifest.xlsx” td$t_files [1] “/home/stvjc/R/x86_64-pc-linux-gnu-library/4.3/gDRimport/extdata/data1/Template_7daytreated.xlsx” [2] “/home/stvjc/R/x86_64-pc-linux-gnu-library/4.3/gDRimport/extdata/data1/Template_Untreated.xlsx”
This is quite unpleasant, in the vignette. You should define an object class that manages the paths, with methods that can use them. You don't have to use S4 but it is recommended.
Hi, We've just merged the PRs with the suggested solution (https://github.com/gdrplatform/gDR/pull/28, https://github.com/gdrplatform/gDRcore/pull/75 and https://github.com/gdrplatform/gDRimport/pull/42).
Hi, @vjcitn and @lshep Thanks in advance for the feedback regarding the current status.
are you bumping version numbers to get new builds?
Hi,
No just to assure all dependencies are up-to-date.
Best, Arek
On Thu, Apr 20, 2023 at 5:42 PM Vince Carey @.***> wrote:
are you bumping version numbers to get new builds?
— Reply to this email directly, view it on GitHub https://github.com/Bioconductor/Contributions/issues/3004#issuecomment-1516555585, or unsubscribe https://github.com/notifications/unsubscribe-auth/AJ2CMZO5DRMY7KTR4EQ56VTXCFKOFANCNFSM6AAAAAAWOKVZ24 . You are receiving this because you were mentioned.Message ID: @.***>
Received a valid push on git.bioconductor.org; starting a build for commit id: 22a5ffd2df729e13a8ca9ce0fd9c837e121579aa
Dear Package contributor,
This is the automated single package builder at bioconductor.org.
Your package has been built on Linux, Mac, and Windows.
On one or more platforms, the build results were: "ERROR, skipped". This may mean there is a problem with the package that you need to fix. Or it may mean that there is a problem with the build system itself.
Please see the build report for more details. This link will be active for 21 days.
Remember: if you submitted your package after July 7th, 2020,
when making changes to your repository push to
git@git.bioconductor.org:packages/gDR
to trigger a new build.
A quick tutorial for setting up remotes and pushing to upstream can be found here.
Received a valid push on git.bioconductor.org; starting a build for commit id: c03ef3bdc5cb7bc644217a0d7fc4fe62ded1352a
Dear Package contributor,
This is the automated single package builder at bioconductor.org.
Your package has been built on Linux, Mac, and Windows.
On one or more platforms, the build results were: "ERROR, skipped". This may mean there is a problem with the package that you need to fix. Or it may mean that there is a problem with the build system itself.
Please see the build report for more details. This link will be active for 21 days.
Remember: if you submitted your package after July 7th, 2020,
when making changes to your repository push to
git@git.bioconductor.org:packages/gDR
to trigger a new build.
A quick tutorial for setting up remotes and pushing to upstream can be found here.
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