Closed Petra-P closed 3 years ago
Hi @Petra-P
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:
Package: ComPrAn
Type: Package
Title: Complexome Profiling Analysis package
Version: 0.99.0
Authors@R:
c(person(given = "Rick",
family = "Scavetta",
role = c("aut"),
email = "rick@scavetta.academy"),
person(given = "Petra",
family = "Palenikova",
role = c("aut", "cre"),
email = "pp451@cam.ac.uk",
comment = c(ORCID = "0000-0002-2465-4370")))
Description: This package is for analysis of SILAC labeled complexome profiling
data. It uses peptide table in tab-delimited format as an input and produces
ready-to-use tables and plots.
License: MIT + file LICENSE
Encoding: UTF-8
Imports:
data.table,
dplyr,
forcats,
ggplot2,
magrittr,
purrr,
tidyr,
rlang,
stringr,
shiny,
DT,
RColorBrewer,
VennDiagram,
rio,
scales,
shinydashboard,
shinyjs,
stats,
tibble,
grid
RoxygenNote: 7.1.1
Suggests:
testthat (>= 2.1.0),
knitr
VignetteBuilder: knitr
biocViews: MassSpectrometry, Proteomics, Visualization
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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/ComPrAn
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: dafda3ab8d29db7408761282f395c66228326517
Dear Package contributor,
This is the automated single package builder at bioconductor.org.
Your package has been built on Linux, Mac, and Windows.
Congratulations! The package built without errors or warnings on all platforms.
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/ComPrAn
to trigger a new build.
A quick tutorial for setting up remotes and pushing to upstream can be found here.
Hi @Petra-P ,
Thanks for submitting ComPrAn. Package looks good and is well documented but I noticed that some plots in the proteinWorkflow.html vignette are empty. The problematic plots are:
Also the SILACcomplexomics.html vignette repeats these 2 sections and has the same problematic figures. Note that this kind of repetition in the documentation should be avoided ("Don't Repeat Yourself (DRY)" principle in software engineering which also applies to the documentation).
Thanks, H.
Received a valid push on git.bioconductor.org; starting a build for commit id: ef9e520c0f343b096a6d3e3c0b00a5a97ec7202f
Dear Package contributor,
This is the automated single package builder at bioconductor.org.
Your package has been built on Linux, Mac, and Windows.
Congratulations! The package built without errors or warnings on all platforms.
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/ComPrAn
to trigger a new build.
A quick tutorial for setting up remotes and pushing to upstream can be found here.
Hi @hpages ,
Thank you very much for your comments. I edited the vignettes, removing the repeated part and replacing it with a link between SILACcomplexomics.html and proteinWorkflow.html.
I am not sure what might be causing the plots to show empty as I was not able to replicate the issue. After running
devtools::install_github("https://github.com/Scavetta/ComPrAn", build_vignettes = TRUE)
browseVignettes("ComPrAn")
I could see both plots in proteinWorkflow.html on Windows (R version 4.0.3 (2020-10-10); Platform: x86_64-w64-mingw32/x64 (64-bit); Running under: Windows 10 x64 (build 19041)) and Linux (R version 4.0.3 (2020-10-10); Platform: x86_64-pc-linux-gnu (64-bit); Running under: Ubuntu 20.04.1 LTS). Is there anything you would suggest to try to identify and solve the issue? Thank you!
Hi @Petra-P ,
It looks like you're using the wrong version of R. You're submitting a package for inclusion to BioC 3.13 which is based on R 4.1 (the current devel version of R) so you need to use that version to develop and test your package. After running:
library(devtools)
devtools::install_github("https://github.com/Scavetta/ComPrAn", build_vignettes=TRUE)
library(ComPrAn)
browseVignettes("ComPrAn")
my sessionInfo() is:
R Under development (unstable) (2021-02-05 r79941)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Ubuntu 20.10
Matrix products: default
BLAS: /home/hpages/R/R-4.1.r79941/lib/libRblas.so
LAPACK: /home/hpages/R/R-4.1.r79941/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] ComPrAn_0.99.2 devtools_2.3.2 usethis_2.0.1
loaded via a namespace (and not attached):
[1] Rcpp_1.0.6 tidyr_1.1.2 prettyunits_1.1.1
[4] ps_1.5.0 assertthat_0.2.1 rprojroot_2.0.2
[7] digest_0.6.27 R6_2.5.0 cellranger_1.1.0
[10] futile.options_1.0.1 ggplot2_3.3.3 pillar_1.4.7
[13] rlang_0.4.10 curl_4.3 readxl_1.3.1
[16] VennDiagram_1.6.20 rstudioapi_0.13 data.table_1.13.6
[19] callr_3.5.1 DT_0.17 shinyjs_2.0.0
[22] desc_1.2.0 stringr_1.4.0 foreign_0.8-81
[25] htmlwidgets_1.5.3 munsell_0.5.0 compiler_4.1.0
[28] pkgconfig_2.0.3 pkgbuild_1.2.0 htmltools_0.5.1.1
[31] tidyselect_1.1.0 tibble_3.0.6 rio_0.5.16
[34] crayon_1.4.1 dplyr_1.0.4 withr_2.4.1
[37] later_1.1.0.1 grid_4.1.0 gtable_0.3.0
[40] lifecycle_1.0.0 DBI_1.1.1 magrittr_2.0.1
[43] formatR_1.7 scales_1.1.1 zip_2.1.1
[46] cli_2.3.0 stringi_1.5.3 cachem_1.0.4
[49] fs_1.5.0 promises_1.2.0.1 remotes_2.2.0
[52] testthat_3.0.2 futile.logger_1.4.3 ellipsis_0.3.1
[55] generics_0.1.0 vctrs_0.3.6 openxlsx_4.2.3
[58] lambda.r_1.2.4 RColorBrewer_1.1-2 tools_4.1.0
[61] forcats_0.5.1 glue_1.4.2 purrr_0.3.4
[64] hms_1.0.0 processx_3.4.5 pkgload_1.1.0
[67] fastmap_1.1.0 colorspace_2.0-0 sessioninfo_1.1.1
[70] shinydashboard_0.7.1 memoise_2.0.0 haven_2.3.1
Best, H.
Hi @Petra-P @hpages
I've tested this on my computer and I can see the points with Bioconductor 3.13.
Best, Marcel
Thanks @LiNk-NY for testing this. Really confusing that you can't reproduce this given that you're using the exact same OS as I do (Ubuntu 20.10).
BTW an easier way to reproduce (for me) is to just run the oneGroupTwoLabelsCoMigration
example:
library(ComPrAn)
example(oneGroupTwoLabelsCoMigration)
# ...
# Hit <Return> to see next plot:
After hitting \<Return> I get the following warning:
Warning message:
In grid.Call.graphics(C_points, x$x, x$y, x$pch, x$size) :
semi-transparency is not supported on this device: reported only once per page
and the following plot:
However, if I use alphaValue=1
:
oneGroupTwoLabelsCoMigration(forAnalysis, max_frac, groupDV, groupName, alphaValue=1)
then everything is fine:
@Petra-P So maybe an easy workaround would be to just set alphaValue
to 1 by default?
@hpaes I am able to output the plot. Could it be differences in the R-devel version? I am not sure what is causing this.
Here are my capabilities()
> capabilities()
jpeg png tiff tcltk X11 aqua
TRUE TRUE TRUE TRUE TRUE FALSE
http/ftp sockets libxml fifo cledit iconv
TRUE TRUE TRUE TRUE TRUE TRUE
NLS Rprof profmem cairo ICU long.double
TRUE TRUE FALSE TRUE TRUE TRUE
libcurl
TRUE
Not sure either. I have the exact same capabilities()
.
FWIW I also tried with an older R-devel installation that I kept around (2020-11-18 r79449) and got the same thing (i.e. an empty plot). Maybe the semi-transparency capability of the X11 device is provided via an additional deb package? I'm starting to suspect a missing deb package in the X11 family.
This problem is real i.e. many users have reported the "semi-transparency is not supported on this device" problem. Until we understand what's going on exactly, let's avoid using alphaValue
< 1.
Received a valid push on git.bioconductor.org; starting a build for commit id: 75eb33a4ee75a72b3e7dac0468d1d3fa40cafc80
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: "WARNINGS". 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/ComPrAn
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: 5f8c1d8c4a17fb2a3311a3fbb885e5c00ca1f12b
Dear Package contributor,
This is the automated single package builder at bioconductor.org.
Your package has been built on Linux, Mac, and Windows.
Congratulations! The package built without errors or warnings on all platforms.
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/ComPrAn
to trigger a new build.
A quick tutorial for setting up remotes and pushing to upstream can be found here.
Hi @hpages @LiNk-NY ,
Thank you for testing the package! I changed the default value of alphaValue
to 1 in both functions to avoid the warning message for now. I also added a CITATION
file as paper describing ComPrAn has been published recently (https://doi.org/10.1016/j.bbabio.2021.148399).
I am getting the semi-transparency waring message on Linux with R 4.1 (session info below). When using Rstudio I was able to display the plot correctly with alphaValue <1 after setting options(bitmapType="cairo")
.
On Windows with R 4.1 plot is displayed fine with alphaValue<1 (session info below).
Best, Petra
Linux sessionInfo():
R Under development (unstable) (2021-02-20 r80030)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Ubuntu 20.04.1 LTS
atrix products: default
BLAS: /usr/local/lib/R/lib/libRblas.so
LAPACK: /usr/local/lib/R/lib/libRlapack.so
locale:
[1] LC_CTYPE=en_US.UTF-8
[2] LC_NUMERIC=C
[3] LC_TIME=sk_SK.UTF-8
[4] LC_COLLATE=en_US.UTF-8
[5] LC_MONETARY=sk_SK.UTF-8
[6] LC_MESSAGES=en_US.UTF-8
[7] LC_PAPER=sk_SK.UTF-8
[8] LC_NAME=C
[9] LC_ADDRESS=C
[10] LC_TELEPHONE=C
[11] LC_MEASUREMENT=sk_SK.UTF-8
[12] LC_IDENTIFICATION=C
attached base packages:
[1] stats graphics grDevices
[4] utils datasets methods
[7] base
other attached packages:
[1] ComPrAn_0.99.2
loaded via a namespace (and not attached):
[1] zip_2.1.1
[2] Rcpp_1.0.6
[3] later_1.1.0.1
[4] cellranger_1.1.0
[5] pillar_1.5.0
[6] compiler_4.1.0
[7] formatR_1.7
[8] RColorBrewer_1.1-2
[9] futile.logger_1.4.3
[10] shinyjs_2.0.0
[11] forcats_0.5.1
[12] futile.options_1.0.1
[13] tools_4.1.0
[14] digest_0.6.27
[15] lifecycle_1.0.0
[16] tibble_3.1.0
[17] gtable_0.3.0
[18] pkgconfig_2.0.3
[19] rlang_0.4.10
[20] openxlsx_4.2.3
[21] curl_4.3
[22] VennDiagram_1.6.20
[23] haven_2.3.1
[24] rio_0.5.16
[25] withr_2.4.1
[26] stringr_1.4.0
[27] dplyr_1.0.4
[28] hms_1.0.0
[29] generics_0.1.0
[30] vctrs_0.3.6
[31] htmlwidgets_1.5.3
[32] shinydashboard_0.7.1
[33] grid_4.1.0
[34] DT_0.17
[35] tidyselect_1.1.0
[36] glue_1.4.2
[37] data.table_1.14.0
[38] R6_2.5.0
[39] fansi_0.4.2
[40] readxl_1.3.1
[41] foreign_0.8-81
[42] farver_2.0.3
[43] tidyr_1.1.2
[44] purrr_0.3.4
[45] ggplot2_3.3.3
[46] lambda.r_1.2.4
[47] magrittr_2.0.1
[48] promises_1.2.0.1
[49] scales_1.1.1
[50] ellipsis_0.3.1
[51] htmltools_0.5.1.1
[52] colorspace_2.0-0
[53] utf8_1.1.4
[54] stringi_1.5.3
[55] munsell_0.5.0
[56] crayon_1.4.1
Windows sessionInfo():
R Under development (unstable) (2021-02-27 r80043)
Platform: x86_64-w64-mingw32/x64 (64-bit)
Running under: Windows 7 x64 (build 7601) Service Pack 1
Matrix products: default
locale:
[1] LC_COLLATE=Slovak_Slovakia.1250 LC_CTYPE=Slovak_Slovakia.1250
[3] LC_MONETARY=Slovak_Slovakia.1250 LC_NUMERIC=C
[5] LC_TIME=Slovak_Slovakia.1250
attached base packages:
[1] stats graphics grDevices utils datasets methods base
other attached packages:
[1] ComPrAn_0.99.4
loaded via a namespace (and not attached):
[1] Rcpp_1.0.6 tidyr_1.1.3 prettyunits_1.1.1
[4] ps_1.5.0 assertthat_0.2.1 rprojroot_2.0.2
[7] digest_0.6.27 utf8_1.1.4 R6_2.5.0
[10] cellranger_1.1.0 futile.options_1.0.1 ggplot2_3.3.3
[13] pillar_1.5.1 rlang_0.4.10 curl_4.3
[16] readxl_1.3.1 VennDiagram_1.6.20 rstudioapi_0.13
[19] data.table_1.14.0 callr_3.5.1 DT_0.17
[22] shinyjs_2.0.0 desc_1.2.0 devtools_2.3.2
[25] stringr_1.4.0 foreign_0.8-81 htmlwidgets_1.5.3
[28] munsell_0.5.0 compiler_4.1.0 pkgconfig_2.0.3
[31] pkgbuild_1.2.0 htmltools_0.5.1.1 tidyselect_1.1.0
[34] tibble_3.1.0 rio_0.5.26 fansi_0.4.2
[37] later_1.1.0.1 crayon_1.4.1 dplyr_1.0.5
[40] withr_2.4.1 grid_4.1.0 gtable_0.3.0
[43] lifecycle_1.0.0 magrittr_2.0.1 formatR_1.7
[46] scales_1.1.1 zip_2.1.1 cli_2.3.1
[49] stringi_1.5.3 cachem_1.0.4 farver_2.1.0
[52] promises_1.2.0.1 fs_1.5.0 remotes_2.2.0
[55] testthat_3.0.2 futile.logger_1.4.3 ellipsis_0.3.1
[58] generics_0.1.0 vctrs_0.3.6 openxlsx_4.2.3
[61] lambda.r_1.2.4 RColorBrewer_1.1-2 tools_4.1.0
[64] forcats_0.5.1 glue_1.4.2 purrr_0.3.4
[67] hms_1.0.0 processx_3.4.5 pkgload_1.2.0
[70] fastmap_1.1.0 colorspace_2.0-0 sessioninfo_1.1.1
[73] shinydashboard_0.7.1 memoise_2.0.0 haven_2.3.1
[76] usethis_2.0.1
Thanks!
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