Closed bhagwataditya closed 4 years ago
Hi @bhagwataditya
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: multicrispr
Title: Multi-locus multi-purpose Crispr/Cas design
Version: 0.99.0
Authors@R: c(person("Aditya", "Bhagwat", NULL, "aditya.bhagwat@mpi-bn.mpg.de", c("aut", "cre")),
person( "Johannes", "Graumann", NULL, 'johannes.graumann@mpi-bn.mpg.de', "sad"),
person( "Mette", "Bentsen", NULL, "mette.bentsen@mpi-bn.mpg.de", "ctb"),
person( "Jens", "Preussner", NULL, "jens.preussner@mpi-bn.mpg.de", "ctb"),
person( "Michael", "Lawrence", NULL, "lawrence.michael@gene.com", "ctb"),
person( "Herve", "Pages", NULL, "hpages@fredhutch.org", "ctb"),
person( "Mario", "Looso", NULL, "mario.looso@mpi-bn.mpg.de", c("sad","rth")))
Description: Contains functions to facilitate the design of a multi-locus Crispr/Cas library.
License: GPL-2
Encoding: UTF-8
LazyData: true
RoxygenNote: 7.1.0
Depends:
R (>= 4.0)
Imports:
assertive,
AnnotationHub,
BiocGenerics,
Biostrings,
BSgenome,
CRISPRseek,
data.table,
GenomeInfoDb,
GenomicFeatures,
GenomicRanges,
ggplot2,
grid,
Gviz,
karyoploteR,
magrittr,
methods,
parallel,
plyranges,
Rbowtie,
reticulate,
rtracklayer,
stringi,
tidyr,
utils
Suggests:
BiocStyle,
BSgenome.Hsapiens.UCSC.hg38,
BSgenome.Mmusculus.UCSC.mm10,
BSgenome.Scerevisiae.UCSC.sacCer1,
dbplyr,
dplyr,
ensembldb,
htmltools,
htmlwidgets,
IRanges,
knitr,
rmarkdown,
testthat,
TxDb.Mmusculus.UCSC.mm10.knownGene
VignetteBuilder: knitr
biocViews: CRISPR, Software
BugReports: https://github.com/loosolab/multicrispr/issues
URL: https://github.com/loosolab/multicrispr
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As preliminary comments
Can you please expand the Description: field of the DESCRIPITION file to provide a more comprehensive abstract of your package?
The large number of dependencies seemed surprising given the focused nature of your package. Please examine these very carefully to evaluate the trade-off between features enabled and maintenance cost.
It never seems like a good idea to run anything as admin, so I was surprised to see the instructions to do so in the vignette. Also consider using basilisk as a 'Bioconductor standard' way of enabling use of python dependencies @LTLA
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: "skipped, ERROR". 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.
By and large, basilisk should be able to handle the Python dependencies that I can see (2.7, azimuth, scikit-learn). The main issues occur on Windows, as they typically do. The success of installation of Python 2.7 on Windows is unpredictable, and installation of Python packages via pip
is dependent on whether non-system DLLs have found their way into the system directories on the user machine.
Thankyou Martin & Aaron, Looking into how to integrate your recommendations. Will get back with an update soon.
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: "skipped, ERROR". 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.
Received a valid push; starting a build. Commits are:
0d5f08c Update vignette
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: "skipped, ERROR". 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.
Thankyou @mtmorgan and @LTLA
I followed your recommendations and:
Regarding the failure to build: this is puzzling to me. I can successfully build it in a win R-devel as well as a linux R-devel environment, without getting the errors of the BioC machines.
Regarding basilisk: thank you for letting me know - looks interesting! That should be unrelated to the current issue of non-building, however. I have taken care in the (current) vignette to not run the python code (it's anyways only an optional last step in the whole gRNA design process). So I would prefer to first get the current vignette and package building.
Thank you for your feedback!
Aditya
Since the vignette is failing, I installed the package
multicrispr master$ bioc-devel CMD INSTALL .
(using R 4.0.0 and BiocManager::install(version = "devel"), making sure
BiocManager::valid()` returns (something close to) TRUE).
I noticed that the git repository contains 'build products', i.e., the file vignettes/designing_grna_libraries.R. This file should not be present, because it will be created when the package is built. Nonetheless, I then ran 'Stangle' on the vignette to get the R code
multicrispr master$ cd vignettes
multicrispr/vignettes master$ bioc-devel CMD Stangle designing_grna_libraries.Rmd
This gave me an up-to-date version of designing_grna_libraries.R. So I started R and sourced that file
multicrispr/vignettes master$ bioc-devel
> source("designing_grna_libraries.R", echo=TRUE)
...
> tfbs0 <- bed_to_granges(bedfile, genome = 'mm10')
Read SRF.bed into GRanges
Error in bed$thickStart : $ operator is invalid for atomic vectors
> traceback()
12: .local(con, format, text, ...)
11: import(FileForFormat(con, format), ...)
10: import(FileForFormat(con, format), ...)
9: import(con, format = "bed", ...)
8: import(con, format = "bed", ...)
7: rtracklayer::import.bed(bedfile, genome = genome)
6: rtracklayer::import.bed(bedfile, genome = genome)
5: bed_to_granges(bedfile, genome = "mm10") at designing_grna_libraries.R#52
4: eval(ei, envir)
3: eval(ei, envir)
2: withVisible(eval(ei, envir))
1: source("designing_grna_libraries.R", echo = TRUE)
digging a little more
> bedfile
[1] "/Users/ma38727/Library/R/4.0/Bioc/3.11/library/multicrispr/extdata/SRF.bed"
> rtracklayer::import(bedfile)
Error: $ operator is invalid for atomic vectors
a little more digging after methods("import")
> debug(import, signature = c("BEDFile", "ANY", "ANY"))
> rtracklayer::import(bedfile)
...
Browse[3]> next
debug: if (!is.null(bed$thickStart)) {
thickEnd <- bed$thickEnd
if (is.null(thickEnd))
thickEnd <- bed$end
bed$thick <- IRanges(bed$thickStart + 1L, thickEnd)
bed$thickStart <- bed$thickEnd <- NULL
}
Browse[3]> next
Error in bed$thickStart : $ operator is invalid for atomic vectors
and the next time round
Browse[2]>
debug: bed <- DataFrame(read.table(con, colClasses = bedClasses, as.is = TRUE,
na.strings = c(".", na.strings), comment.char = "", sep = sep,
quote = ""))
Browse[2]>
debug: colnames(bed) <- bedNames[bedNames %in% colnames]
Browse[2]> class(bed)
[1] "DFrame"
attr(,"package")
[1] "S4Vectors"
Browse[2]> dim(bed)
[1] 3 1
Browse[2]> bed
DataFrame with 3 rows and 1 column
V1
<character>
1 version https://git-lfs.github.com/spec/v1
2 oid sha256:2e5c03b513ea39388a19c7b7aa3118320d644bfc81085d51a7170e2e155744a6
3 size 91414
which is looking kind of strange -- column is advertised as V1
but actually
Browse[2]> names(bed)
[1] "chrom"
Browse[2]> bed$chrom
[1] "version https://git-lfs.github.com/spec/v1"
[2] "oid sha256:2e5c03b513ea39388a19c7b7aa3118320d644bfc81085d51a7170e2e155744a6"
[3] "size 91414"
and there's no thickStart
column...
Browse[2]> bed$thickStart
Error in bed$thickStart : $ operator is invalid for atomic vectors
This seems very funky. So I confirmed that
BiocManager::valid()
returns TRUE, turned off debugging
> undebug(import, signature = c("BEDFile", "ANY", "ANY"))
and checked whether the examples on the import.bed
help page ran...
example(import.bed)
They did run successfully.
A first guess is that SRF.bed is malformed. Other than that, I'm at a loss, and call on @lawremi or perhaps @hpages for advice... The simple reproducible example is, in a new R session,
$ bioc-devel
> rtracklayer::import("multicrispr/inst/extdata/SRF.bed")
Error in bed$thickStart : $ operator is invalid for atomic vectors
Thankyou @mtmorgan!
I can reproduce the error with the installed data file on rocker-devel:
> rtracklayer::import.bed(system.file("extdata/SRF.bed", package = 'multicrispr'))
Error: $ operator is invalid for atomic vectors
Interestingly enough, the source data file does not give any issues:
> rtracklayer::import.bed("inst/extdata/SRF.bed")
GRanges object with 1974 ranges and 2 metadata columns:
seqnames ranges strand | name score
<Rle> <IRanges> <Rle> | <character> <numeric>
[1] chr2 83972890-83972905 + | SRF_MA0083.3 8.61532
... ... ... ... . ... ...
[1974] chr4 106237089-106237104 + | SRF_MA0083.3 9.73780
-------
seqinfo: 21 sequences from an unspecified genome; no seqlengths
What could be happening?
Aditya
Oh, this seems to be a git-lfs issue. When I vim the installed file, I get:
> vim /usr/local/lib/R/site-library/multicrispr/extdata/SRF.bed
version https://git-lfs.github.com/spec/v1
oid sha256:2e5c03b513ea39388a19c7b7aa3118320d644bfc81085d51a7170e2e155744a6
size 91414
When I vim the source file, I get:
> vim multicrispr/inst/extdata/SRF.bed
chr2 83972889 83972905 SRF_MA0083.3 8.61532 +
chr1 85603908 85603924 SRF_MA0083.3 9.7378 -
chr17 70963622 70963638 SRF_MA0083.3 9.7378 -
...
So I guess I should remove these files from git LFS tracking - will do and then push
Yes, the build system is just going to git clone
without LFS support.
If these are large files then probably you should either (a) identify a (much) more modest subset for demonstrating your software or (b) make the files available via ExperimentHub as a package.
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: "skipped, ERROR". 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.
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: "skipped, ERROR". 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.
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: "TIMEOUT, 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.
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: "skipped, ERROR". 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.
Received a valid push; starting a build. Commits are:
808d04a Re-roxygenize
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.
Received a valid push; starting a build. Commits are:
fb5063a AnnotationHub: Imports -> Suggests
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.
Remove commented out code.
Use BiocParallel
instead of parallel::mclapply()
.
Are you sure you have cut down dependencies enough? There are still quite a few. Loading the package takes a while.
Hi Nitesh, thank you for your nice feedback :-), which I followed up on:
R
extdata
Okay then, let me push my updates
Received a valid push; starting a build. Commits are:
ffa1738 Bump version
Dear Package contributor,
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