biomartr package #93
Comments
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Thanks for your submission @HajkD - discussing and will get back soon |
Editor checks:
Editor commentsThanks for your submission! Currently seeking reviewers. Reviewers: @naupaka @grimbough |
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moving ahead with @naupaka as reviewer - haven't been able to get anyone else |
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Many thanks! I am very much looking forward to receiving feedback. |
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Added @grimbough as second reviewer, thanks @grimbough ! As a reminder here are links to the recently updated reviewing and packaging guides and to the review template. |
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@naupaka @grimbough Please get your reviews in soon - due on 13 March - and thanks for reviewing ! 😸 |
Package ReviewPlease check off boxes as applicable, and elaborate in comments below. Your review is not limited to these topics, as described in the reviewer guide
DocumentationThe package includes all the following forms of documentation:
Functionality
Final approval (post-review)
Estimated hours spent reviewing: 8 hours Review CommentsBefore I start my review, I want to state that although there is no conflict of interest and I have never worked on this package, I am a contributer to the biomaRt package, and so my review may be skewed towards functionality that overlaps with that. The biomartr package is essentially a 'meta-package' and tries to present a consistent interface to a variety of online resources that provide to genomic data. It does this either by accessing their APIs directly, or by providing a wrapper around existing R packages like biomaRt. I actually find the package name a little misleading, since this does way more than just provide an R interface to the BioMart API. Perhaps that was the original intention for the package, but the present functionality exceeds this. It's probably a bit late to change this though given there are existing publications referring to it. One other small semantic point, which you see a lot, is that this package provides access to 'Ensembl Biomart', rather than accessing Biomart services in general. There are in fact many other databases that use Biomart as a way to query their data e.g. SalmonDB or Pancreas Expression Database, which this package currently doesn't provide access to. This is particularly true since the centralised access via Biomart.org no longer exists, and it might be worth clarifying this in the README and Introductory vignette. Build/InstallI found the installation to work fine. There are clear instructions in the README file, which detail how to install both the stable version in CRAN, and the developmental version from Github. This review is conducted on the version labeled 0.4.0 from Github. The author might be interested to know that you can use and similarly for github One other thing to note is that the importing of functions from biomaRt and Biostrings is never defined explicitly. They are mentioned in the installation instructions and their functions are accessed using the double colon operator e.g. Examples and testsMost functions have examples, and those that I tested manually worked. However, they are all set to not run with DONTRUN flags, so it is difficult to run them in an automated fashion. This also means they aren't run when the package is built and check, so there is a chance that some no longer execute successfully. I would certainly encourage the package maintainers to make it that more of the examples are run, although I appreciate that they probably take a long time to execute given almost all are retrieving online data sets. Running the set of tests that accompany the package to over 30 minutes for me. When running
Documentation and vignettesThe vignettes are generally well written and cover a variety of use cases. The vignette naming is also based around these use cases, which I guess makes sense if you approach the package with a particular research domain in mind, but is not so helpful if you a looking for how to access a specific service. For example, if I know I want to query Ensembl BioMart (which doesn't seem unreasonable given the package name) it doesn't feel intuitive to me that I have to look in 'Evolutionary Transcriptomics' to find an example of accessing that particular resource. This would be somewhat mitigated by the suggestion to include services in the function names, so it is at least easier to find the appropriate manual page. I would highly recommend making more of the vignette examples evaluated when the Rmarkdown documents are rendered. Over time the contents of the databases can change, and having static output in the vignettes can lead to confusion among users, when what they see when running a code block no longer matches what they see in the documentation. For example running the command Does the package comply with the ROpenSci packaging guide?Function/variable naming & general syntaxIn general the code is pretty easy to read, with sensible variable names and neatly structured code. However, the function naming within the package seems to be inconsistent. There are examples of camelCaps, snake_case and period.separated. Personally I would avoid using period.separated since there is the potential to conflict with the S3 method dispatch system, but you can find at least one style guide to support each. However, it would be nice to be consistent within the package. I also think from a user view point that some function names could perhaps be more explicit about the resource they are accessing. e.g. There are also a few examples of accessing slots in S4 objects using Documentation styleROxygen is used throughout to document the functions in the same file as the code itself. When viewing this as as a programmer (rather than a user) this makes understanding the intention of the function and its arguments much easier than using the traditional way of writing .Rd files manually. I am a definite fan! Console messagesThere are quite a few instances of The Is there code duplication in the package that should be reduced?There are a few instances where variables such as file names are created multiple times throughout the same function. For example
Similarly there is a lot of overlap between getENSEMBL.Seq.R and getENSEMBLGENOMES.Seq.R. I wonder if these could be combined, and the requested host used to select the few lines that are different? Recommended scaffoldingHTTP requests and processing are a core component of this package. These are done using the |
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thanks very much for your review @grimbough ! |
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Okay, thanks for the update @naupaka |
Package ReviewPlease check off boxes as applicable, and elaborate in comments below. Your review is not limited to these topics, as described in the reviewer guide
DocumentationThe package includes all the following forms of documentation:
Functionality
Final approval (post-review)
Estimated hours spent reviewing: 12 hours Review CommentsI should say right up here at the front that this is my first review for ROpenSci, so it probably took me a bit longer than others might have to get up to speed. It's also a relatively large package in terms of the number of functions it exposes to the user, and it took me a while to figure out how the parts fit together. I'm sure I missed things, but hopefully having me muddle through the codebase will provide some opportunities to smooth a few rough edges. The goal of the package, as I understand it, is to provide a higher-level interface for programmatically downloading sequence or other datasets from major repositories. Overall, I think the package fills a useful niche and I plan to use it for my own research needs in the future. I hope that the commentary below is helpful. I downloaded and read the Bioinformatics paper that describes the package. I found it helpful for understanding the goals of the package, and how it differs from biomaRt, which was something I was initially confused about. I think it would be nice to clarify in the README and elsewhere that the queries work, for the most part (as far as I understand it), against NCBI or EMSEMBL, and not from any of the many other sources that have a BioMart interface (as @grimbough pointed out). For example, I am interested in getting data from the BioMart interface to JGI's Phytozome, since they have a 3.0 version of the Populus trichocarpa genome (the NCBI version is still at 2.0), but that is not possible, I believe, with this package (feature request 😃). Another thing that I didn't see, but I think would be useful, would be to modify Minor comments and other issuesREADMENo Travis badge in README. DocumentationWhile all exported functions have roxygen-generated documentation, some internal functions have no comments or documentation, e.g. I also agree with @grimbough that it would be ideal if at least some of the example code in the documentation could actually be run. The output from CodeFunction/variable naming & general syntax
Suggestions
── GP biomartr ──────────────────────────────────────────────────────────────────────────
It is good practice to
✖ write unit tests for all functions, and all package code in general. 0% of
code lines are covered by test cases.
R/biomart.R:49:NA
R/biomart.R:50:NA
R/biomart.R:51:NA
R/biomart.R:53:NA
R/biomart.R:54:NA
... and 4297 more lines
✖ write short and simple functions. These functions have high cyclomatic
complexity:listGenomes (78), meta.retrieval (63).
✖ avoid long code lines, it is bad for readability. Also, many people prefer
editor windows that are about 80 characters wide. Try make your lines
shorter than 80 characters
R/biomart.R:71:1
R/biomart.R:72:1
R/connected.to.internet.R:5:1
R/download_database.R:38:1
R/download_database.R:52:1
... and 434 more lines
✖ avoid sapply(), it is not type safe. It might return a vector, or a list,
depending on the input data. Consider using vapply() instead.
R/download_database_all.R:21:5
R/download_database.R:31:35
R/getMetaGenomeAnnotations.R:96:31
R/getMetaGenomes.R:96:31
R/listDatabases.R:78:29
... and 11 more lines
✖ avoid 1:length(...), 1:nrow(...), 1:ncol(...), 1:NROW(...) and 1:NCOL(...)
expressions. They are error prone and result 1:0 if the expression on the
right hand side is zero. Use seq_len() or seq_along() instead.
R/getAttributes.R:99:36
R/getDatasets.R:55:39
R/getFilters.R:99:40
R/organismAttributes.R:79:39
R/organismFilters.R:75:43
... and 2 more lines
✖ not import packages as a whole, as this can cause name clashes between the
imported packages. Instead, import only the specific functions you need.
✖ fix this R CMD check NOTE: Namespace in Imports field not imported from:
‘stringi’ All declared Imports should be used.TestsA number of the tests fail for me when run with either ==> devtools::check(document = FALSE)
Setting env vars ---------------------------------------------------------------
CFLAGS : -Wall -pedantic
CXXFLAGS: -Wall -pedantic
Building biomartr --------------------------------------------------------------
'/usr/local/Cellar/r/3.3.3/R.framework/Resources/bin/R' --no-site-file \
--no-environ --no-save --no-restore --quiet CMD build \
'/Users/naupaka/git/ROpenSci/biomartr' --no-resave-data --no-manual
* checking for file ‘/Users/naupaka/git/ROpenSci/biomartr/DESCRIPTION’ ... OK
* preparing ‘biomartr’:
* checking DESCRIPTION meta-information ... OK
* installing the package to build vignettes
* creating vignettes ... OK
* checking for LF line-endings in source and make files
* checking for empty or unneeded directories
* building ‘biomartr_0.4.0.tar.gz’
Setting env vars ---------------------------------------------------------------
_R_CHECK_CRAN_INCOMING_USE_ASPELL_: TRUE
_R_CHECK_CRAN_INCOMING_ : FALSE
_R_CHECK_FORCE_SUGGESTS_ : FALSE
Checking biomartr --------------------------------------------------------------
'/usr/local/Cellar/r/3.3.3/R.framework/Resources/bin/R' --no-site-file \
--no-environ --no-save --no-restore --quiet CMD check \
'/var/folders/1y/8s_b2fx520sgj5f3j9fjwg880000gn/T//RtmpyLUWwj/biomartr_0.4.0.tar.gz' \
--as-cran --timings --no-manual
* using log directory ‘/Users/naupaka/git/ROpenSci/biomartr.Rcheck’
* using R version 3.3.3 (2017-03-06)
* using platform: x86_64-apple-darwin16.4.0 (64-bit)
* using session charset: UTF-8
* using options ‘--no-manual --as-cran’
* checking for file ‘biomartr/DESCRIPTION’ ... OK
* this is package ‘biomartr’ version ‘0.4.0’
* package encoding: UTF-8
* checking package namespace information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for executable files ... OK
* checking for hidden files and directories ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘biomartr’ can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking R files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* checking whether the package can be loaded ... OK
* checking whether the package can be loaded with stated dependencies ... OK
* checking whether the package can be unloaded cleanly ... OK
* checking whether the namespace can be loaded with stated dependencies ... OK
* checking whether the namespace can be unloaded cleanly ... OK
* checking loading without being on the library search path ... OK
* checking dependencies in R code ... OK
* 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 line widths ... 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
WARNING
‘qpdf’ is needed for checks on size reduction of PDFs
* checking installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
Running ‘testthat.R’ [147s/511s]
ERROR
Running the tests in ‘tests/testthat.R’ failed.
Last 13 lines of output:
4: tryCatchOne(expr, names, parentenv, handlers[[1L]])
5: value[[3L]](cond)
6: stop(paste0("File ", file, " could not be read properly. \n", "Please make sure that ",
file, " contains only amino acid sequences and is in ", format, " format."),
call. = FALSE)
testthat results ================================================================
OK: 35 SKIPPED: 0 FAILED: 4
1. Failure: The download.database() throws error when wrong input database is specified.. (@test-download.database.R#9)
2. Error: The getGFF() interface works properly.. (@test-getGFF.R#31)
3. Failure: The getGFF() error messages work properly.. (@test-getGFF.R#41)
4. Error: The getProteome() interface works properly.. (@test-getProteome.R#24)
Error: testthat unit tests failed
Execution halted
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in ‘inst/doc’ ... OK
* checking re-building of vignette outputs ... OK
* DONE
Status: 1 ERROR, 1 WARNING
See
‘/Users/naupaka/git/ROpenSci/biomartr.Rcheck/00check.log’
for details.
R CMD check results
1 error | 0 warnings | 0 notes
checking tests ... ERROR
Running ‘testthat.R’ [147s/511s]
Running the tests in ‘tests/testthat.R’ failed.
Last 13 lines of output:
4: tryCatchOne(expr, names, parentenv, handlers[[1L]])
5: value[[3L]](cond)
6: stop(paste0("File ", file, " could not be read properly. \n", "Please make sure that ",
file, " contains only amino acid sequences and is in ", format, " format."),
call. = FALSE)
testthat results ================================================================
OK: 35 SKIPPED: 0 FAILED: 4
1. Failure: The download.database() throws error when wrong input database is specified.. (@test-download.database.R#9)
2. Error: The getGFF() interface works properly.. (@test-getGFF.R#31)
3. Failure: The getGFF() error messages work properly.. (@test-getGFF.R#41)
4. Error: The getProteome() interface works properly.. (@test-getProteome.R#24)
Error: testthat unit tests failed
Execution halted
R CMD check succeededMinor documentation issuesLooks like there is a non-ASCII character in the copied tibble output in one of the verbatim blocks in the Functional Annotation vignette (non-executing). ==> devtools::document(roclets=c('rd', 'collate', 'namespace', 'vignette'))
Updating biomartr documentation
Loading biomartr
Updating vignettes
Rebuilding BioMart_Examples.Rmd
Rebuilding Database_Retrieval.Rmd
Rebuilding Functional_Annotation.Rmd
Error in tools::buildVignette(vign, dirname(vign), tangle = FALSE, clean = FALSE) :
Vignette 'Functional_Annotation' is non-ASCII but has no declared encoding
Calls: suppressPackageStartupMessages ... roclet_output.roclet_vignette -> vign_update_all -> vapply -> FUN -> <Anonymous>
Execution halted
Exited with status 1.> tools::showNonASCII(readLines("vignettes/Functional_Annotation.Rmd"))
# 566: A tibble: 6 <c3><97> 4Repeated "No encoding supplied" warnings> organismBM(organism = "Homo sapiens")
No encoding supplied: defaulting to UTF-8.
No encoding supplied: defaulting to UTF-8.
No encoding supplied: defaulting to UTF-8.
No encoding supplied: defaulting to UTF-8.
# A tibble: 12 × 5
organism_name
<chr>
1 hsapiens
2 hsapiens
3 hsapiens
4 hsapiens
5 hsapiens
6 hsapiens
7 hsapiens
8 hsapiens
9 hsapiens
10 hsapiens
11 hsapiens
12 hsapiens
# ... with 4 more variables: description <chr>, mart <chr>, dataset <chr>,
# version <chr>Need line break before line 33 in Introduction.Rmd, or markdown header doesn't render properly.Error when downloading assembly statsSometimes when I would try to run a command, I'd get errors like this. I was connected to the Internet at the time, and similar commands run before and afterwards worked fine. Sometimes the same command, run a second time, worked fine even though it failed at first. Maybe something about the timeout before waiting for a server response could be tweaked to reduce the likelihood of premature failure? > meta.retrieval(kingdom = "plant",
db = "refseq",
type = "assemblystats",
combine = TRUE)
Error: The FTP site 'ftp://ftp.ncbi.nlm.nih.gov/' cannot be reached. Are you connected to the internet? Is the the FTP site 'ftp://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/001/190/045/GCF_001190045.1_Vigan1.1/GCF_001190045.1_Vigan1.1_assembly_stats.txt' currently available?
In addition: Warning message:
In download.file(url, ...) :
URL 'ftp://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/001/190/045/GCF_001190045.1_Vigan1.1/GCF_001190045.1_Vigan1.1_assembly_stats.txt': status was 'Weird server reply'Session InfoTested with commit 2570b0d3296 on master branch from https://github.com/HajkD/biomartr > sessionInfo()
R version 3.3.3 (2017-03-06)
Platform: x86_64-apple-darwin16.4.0 (64-bit)
Running under: macOS Sierra 10.12.3
locale:
[1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8
attached base packages:
[1] stats graphics grDevices utils datasets methods base
other attached packages:
[1] biomartr_0.4.0
loaded via a namespace (and not attached):
[1] Rcpp_0.12.9 IRanges_2.8.1 XML_3.98-1.5 Biostrings_2.42.1 digest_0.6.12
[6] bitops_1.0-6 DBI_0.6 stats4_3.3.3 RSQLite_1.1-2 zlibbioc_1.20.0
[11] curl_2.3 XVector_0.14.0 S4Vectors_0.12.1 tools_3.3.3 Biobase_2.34.0
[16] biomaRt_2.30.0 RCurl_1.95-4.8 parallel_3.3.3 BiocGenerics_0.20.0 AnnotationDbi_1.36.2
[21] memoise_1.0.0 |
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Dear @sckott, Thank you very much for retrieving two valuable and in-depth reviews from @grimbough and @naupaka for the I am very happy to see that both reviewers appreciate the functionality of I already started to incorporate the suggestions made by @grimbough and will now start to address all issues raised by @naupaka. I highly appreciate the time the reviewers took to generate an in-depth code review and I will now work on a detailed response letter. Kind regards, |
Response to Package ReviewsDear @sckott, I am very grateful for receiving two valuable reviews from @grimbough and @naupaka. I hope that I could address all points sufficiently so that I would like to thank you and both reviewers for your detailed and constructive Kind regards, Response to reviewer 1 (@grimbough)General comments
Response: I agree. Initially, I focused on the BioMart database, but then it closed its service and the NCBI and ENSEMBL databases took over parts of its role and diversified their services as well and I started to extend the functionality of
Response: Many thanks for pointing this out to me. I now made this point clear in the introductory vignette. Build/Install
Response: This is a great suggestion. I now use the
Response: I now explicitly import
Response: Thank you so much for pointing this out to me, but to be honest, I am not sure how to run these download commands while following the CRAN policy that states that examples should terminate within 5 sec. In my initial CRAN submission, I didn't have
Response: I also explored this peculiarity and fixed the unit tests. Documentation and vignettes
Response: I agree and now renamed the vignette to
Response: I agree, and now vignette examples are evaluated when the Rmarkdown documents are rendered. Function/variable naming & general syntax
Response: Thanks for pointing this out to me. In the next versions of
Response: I renamed the Console messages
Response: I agree and now consistently use Is there code duplication in the package that should be reduced?
Response: I now store
Response: Due to the differences in the internal folder structure of the ENSEMBL and ENSEMBLGENOMES servers I had to implement special cases and thus this code redundancy was on purpose to have a better overview for code maintainence. Response to reviewer 2 (@naupaka)Review Comments
Response: I agree and I changed it according to @grimbough's point. The JGI's Phytozome request is taken (ropensci/biomartr#9) and since I am working with plant genomes myself I will try my best to provide some interface functions :D .
Response: This is a functionality extension request. I am happy to implement it for the next README
Response: Travis badge is now included in README.
Response: Many thanks for pointing this out to me. I now commented all internal functions and used
Response: I agree, but please see my response to @grimbough concerning the 5s CRAN policy. Code
Response: As stated above, I now clearly write in the vignettes which databases
Response: I now consistently use Tests
Response: I fixed the corrupt unit tests and now
Response: Thank you so much for detecting this non-ASCII character. It is fixed now.
Response: I included the line break.
Response: The encoding is fixed now.
Response: Thank you so much for pointing this server timeout issue out to me. I now implemented a customized download function which uses the best download tool for the underlying operating system. I hope that this issue is now resolved. |
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@HajkD thanks for your changes and detailed comments
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Dear @sckott, Thank you so much for your suggestions. I will address all comments and will come back to you as soon as I finished. Best wishes, |
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thanks @HajkD |
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Dear @sckott, I addressed all comments and issues and incorporated all changes into the new version of the I hope that I could address all points sufficiently so that Please find my detailed response below. Thank you so much for all your support. Kind regards, Hajk P.S. I just want to make you aware that the Ensembl Services are currently
Response: I tried to solve the running time issue by choosing example test cases that
Response: I agree and now replaced all
Response: A package level manual file is now included and as suggested can be accessed via
Response: I now spent a significant amount of time on increasing the test coverage and will continue to improve it in the future.
Response: Most tests cover the functionality of data retrieval functions, so to reduce
Response: I absolutely agree and see where your confusion comes from. I now commented and specified the unit tests more clearly, so that no confusion exists on what part of the function is actually tested. |
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@grimbough @naupaka Are you happy with changes made? Anything else? Looking over your changes now @HajkD |
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I probably won't have a chance to take a look till later this week. I'll make another pass through then to make sure all works as expected on my machine - seems like all the major points were addressed. |
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yep, i'll rerun tests and report back |
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same error again. DO you get that test error on travis. Have you tried Appveyor? Or r-hub ? |
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Hm, that's strange. Yes, Travis passes. I just committed today -> https://travis-ci.org/HajkD/biomartr/builds/223596728 . I haven't tried rhub or Appveyor yet, but I can run it there as well if you like. |
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What platform are you on? windows? mac? linux? |
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mac |
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Dear @sckott I now also ran an r-hub check and everything seems to pass: https://builder.r-hub.io/status/biomartr_0.5.0.tar.gz-e5116cc3ef554c2db801cbbaa3be1e0f . |
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@HajkD thanks for making many of the recommended changes. Most all of the things I mentioned the first time around are now fixed. I'm still having issues with getting things to work smoothly with Unless maybe this is something insidious that snuck in because of my recent update to R 3.4.0? My system info is below, and I was using commit ca36885e2 on master for these tests. Output from
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thanks for the input @naupaka |
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Dear @naupaka Thank you so much for pointing this shortcoming out to me. Many thanks! |
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@HajkD Any progress on this? Any questions for us? |
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Hi @sckott, Please accept my apologies for my late response. I was caught up in another project that required my immediate attention. Nevertheless, I worked on the remaining While digging deeper into the issue I noticed that the NCBI and ENSEMBL databases don't provide very stable APIs. Servers are frequently maintained and sometimes down for several days. Hence, it is impossible to resolve this issue from my side. However, I now implemented warnings that will occur when connections are not stable or whenever the server is down. I am very happy for any suggestions on how I can improve the In future versions, I also plan to implement I now run When running * using log directory ‘/private/var/folders/3x/6bbw6ds1039gpwny1m0hn8r80000gp/T/RtmpEQJf3b/biomartr.Rcheck’
* using R version 3.4.0 (2017-04-21)
* using platform: x86_64-apple-darwin15.6.0 (64-bit)
* using session charset: UTF-8
* using options ‘--no-manual --as-cran’
* checking for file ‘biomartr/DESCRIPTION’ ... OK
* this is package ‘biomartr’ version ‘0.5.9000’
* package encoding: UTF-8
* checking package namespace information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for executable files ... OK
* checking for hidden files and directories ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘biomartr’ can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking R files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* checking whether the package can be loaded ... OK
* checking whether the package can be loaded with stated dependencies ... OK
* checking whether the package can be unloaded cleanly ... OK
* checking whether the namespace can be loaded with stated dependencies ... OK
* checking whether the namespace can be unloaded cleanly ... OK
* checking dependencies in R code ... OK
* 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 line widths ... 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 installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
Running ‘testthat.R’ [95s/460s]
OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in ‘inst/doc’ ... OK
* checking re-building of vignette outputs ... OK
* DONE
Status: OK
R CMD check results
0 errors | 0 warnings | 0 notesI would be truly grateful if you could test again on your system if the check runs smoothly now. I hope that you can now consider I would like to thank all of you for your time a detailed code review. It helped me a lot to significantly improve the Kind regards, |
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@HajkD Looks good to me, checked locally and all seems fine. approved! |
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Thanks very much for your submission. Remaining steps:
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Dear @sckott I am very grateful for your approval and I very much look forward to collaborating with you and the rOpenSci community. I already transferred the package and would be very interested in a blog post for the more general audience (https://ropensci.org/blog/). Thank you so much for coordinating everything. I truly appreciate it. Kind regards, |
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Great!
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@HajkD let me know if you have any questions about the blog post |
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Many thanks, @sckott. I am quite busy in the past weeks, but I will try to write a post by today. So far, your directions are very clear, but I will happily take your offer to help me in case I get stuck :) |
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Hello @HajkD. Just wanted to say how happy I am that you will contribute a post about |
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Hello @stefaniebutland , Thank you so much for your great feedback :) I truly hope that this package will become a small puzzle stone to help to tackle the reproducibility crisis in biomedical research and also to speed up large-scale genomics studies. If it's useful then I am happy about any collaboration to extend the |
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Hi @sckott , I am very sorry that I still didn't manage to find some quiet time to write a proper blog post. I am quite caught up in a paper revision and collaborations right now. Many thanks for your patience and support :) Kind regards, |
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@HajkD another week is fine, no rush at all! actually, @stefaniebutland when could we fit his post in the blog schedule? |
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@HajkD Could you give me an idea of a month and week that would work for you? I'll work with that to assign you a date to provide a draft and post date. Cheers. |
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Dear @sckott and @stefaniebutland , Thank you so much for your prompt reply and for all your support! @stefaniebutland: Would the week between 03.07. - 09.07. work for you? I could deliver a blog post on any day during that week. I truly appreciate all your efforts and for helping me to schedule the post :) Kind regards, |
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@HajkD A draft in the week of 03.07. - 09.07 would work well. Tentative post date would be Tues July 18. This would give us time to give you feedback on your draft post. |
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Dear @stefaniebutland Many thanks. This sounds perfect. I will post my draft between 03.07. - 09.07 and very much look forward to receiving your feedback. Kind regards, |
Summary
The
biomartrpackage provides researchers with a useful tool for the efficient, straightforward and reproducible handling of large-scale meta-genomic data from NCBI and ENSEMBL databases and intuitive organism centered interface functions for retrieving functional annotation information from the BioMart database. In general, the package promotes computational reproducibility in genomics studies.https://github.com/HajkD/biomartr
Life scientists working with genomic data.
The R packages
seqinrandbiomaRtwere previous attempts to provide parts of thebiomartrfunctionality. Theseqinrpackage aims to automate sequence retrieval in R but is not designed for meta-genomic approaches and does not include functional annotation. ThebiomaRtpackage aims to provide functional annotation methods but these are also not designed for meta-genomic approaches and are not easy to use for non-programming experts. The major advantage ofbiomartris that it does not require profound programming expertise and vastly extends the functionality of both packages:seqinrandbiomaRt. It is optimized to handle large-scale genomic and meta-genomic data using simple and straightforward commands that are useful for life scientists. The functionality provided bybiomartraims to promote computational reproducibility among life scientists without profound programming expertise. This is not achieved by the packagesseqinrandbiomaRtwhich are designed for bioinformaticians and other computationally trained researchers.Requirements
Confirm each of the following by checking the box. This package:
Publication options
paper.mdwith a high-level description in the package root or ininst/.Detail
Does
R CMD check(ordevtools::check()) succeed? Paste and describe any errors or warnings:Does the package conform to rOpenSci packaging guidelines? Please describe any exceptions:
If this is a resubmission following rejection, please explain the change in circumstances:
Is the first submission.
None declared.
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