scQTLtools #3515
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Hi @XFWuCN Thanks for submitting your package. We are taking a quick The DESCRIPTION file for this package is: |
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If this package is working with Single Cell Data, it should work with the standard Bioconductor class SingleCellExperiment. See https://contributions.bioconductor.org/important-bioconductor-package-development-features.html particularly interop with Bioconductor classes. |
lshep
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3e. pending pre-review changes
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It will also be necessary to provide an abstract/intro section in your vignette that provides motivation for inclusion in Bioconductor and a review and comparison to existing Bioconductor packages with similar functionality or |
Thank you for the review, we're working on it. |
Hi, we‘ve edit the |
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To be specific,
Thank you for the review. |
lshep
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pre-check passed
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Your package has been added to git.bioconductor.org to continue the IMPORTANT: Please read this documentation for setting Bioconductor utilized your github ssh-keys for git.bioconductor.org |
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Dear Package contributor, This is the automated single package builder at bioconductor.org. Your package has been built on the Bioconductor Single Package Builder. Congratulations! The package built without errors or warnings Please see the build report for more details. The following are build products from R CMD build on the Single Package Builder: Links above active for 21 days. Remember: if you submitted your package after July 7th, 2020, |
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A reviewer has been assigned to your package for an indepth review. |
Package 'scQTLtools' ReviewThank you for submitting your package to Bioconductor. The package passed check and build. However there are several things need to be fixed. Please try to answer the comments line by line when you are ready for a second review. unacceptable files
General package development
R code
Documentation\
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Received a valid push on git.bioconductor.org; starting a build for commit id: bf41881f34dd885f2bdd78a355f04ec860267240 |
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Dear Package contributor, This is the automated single package builder at bioconductor.org. Your package has been built on the Bioconductor Single Package Builder. On one or more platforms, the build results were: "WARNINGS". Please see the build report for more details. The following are build products from R CMD build on the Single Package Builder: Links above active for 21 days. Remember: if you submitted your package after July 7th, 2020, |
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Received a valid push on git.bioconductor.org; starting a build for commit id: ddfe60082c6d3bdcf424cdf3300f49f46a38cd32 |
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We push the code again, this time we split the long function into small functions, making each function within 50 lines. |
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Dear Package contributor, This is the automated single package builder at bioconductor.org. Your package has been built on the Bioconductor Single Package Builder. On one or more platforms, the build results were: "WARNINGS". Please see the build report for more details. The following are build products from R CMD build on the Single Package Builder: Links above active for 21 days. Remember: if you submitted your package after July 7th, 2020, |
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Sorry, but I don't see any "WAENINGS" or "NOTES" in build report |
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indeed. There seems to be a bug that we will investigate why a warning appears |
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Okay, thank you for your efforts. If there are any problems with the package, please let me know and we will reply positively. |
Package 'scQTLtools' ReviewThe package passed check and build. It is in pretty good shape. Please try to answer the comments line by line when you are ready for a second review. R code
Documentation
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Received a valid push on git.bioconductor.org; starting a build for commit id: 927f2509fe13f5f36e60a87dba430f5f0198dc2e |
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We are still working on it. |
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Dear Package contributor, This is the automated single package builder at bioconductor.org. Your package has been built on the Bioconductor Single Package Builder. On one or more platforms, the build results were: "WARNINGS". Please see the build report for more details. The following are build products from R CMD build on the Single Package Builder: Links above active for 21 days. Remember: if you submitted your package after July 7th, 2020, |
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Hi @XFWuCN , See the warning in this build, This is the reason why I suggest you to make mart as a separate parameter. However, a separate parameter will not always work. You may want to handle this kind of error in the examples. |
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Received a valid push on git.bioconductor.org; starting a build for commit id: fc63fdbf59df16dd05db49272ec811663a54ddf6 |
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Hi @jianhong, thank you for the review. Apologies for the delay in our response. Our modifications and answers are as follows: R code
To accommodate users who may encounter difficulties in connecting to the main database but need to use mirror sites, we have added two new parameters, For example: snp_mart <- useEnsembl(biomart = "snps",
dataset = "hsapiens_snp",
mirror = 'asia')Do my understandings and modifications seem correct to you? Please let me know if you have any further suggestions, or if there are any additional changes needed. Documentation
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Dear Package contributor, This is the automated single package builder at bioconductor.org. Your package has been built on the Bioconductor Single Package Builder. On one or more platforms, the build results were: "ERROR". Please see the build report for more details. The following are build products from R CMD build on the Single Package Builder: Links above active for 21 days. Remember: if you submitted your package after July 7th, 2020, |
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Received a valid push on git.bioconductor.org; starting a build for commit id: 11969008c5294083a9c548c66b29b91abb544a13 |
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Dear Package contributor, This is the automated single package builder at bioconductor.org. Your package has been built on the Bioconductor Single Package Builder. On one or more platforms, the build results were: "ERROR". Please see the build report for more details. The following are build products from R CMD build on the Single Package Builder: Links above active for 21 days. Remember: if you submitted your package after July 7th, 2020, |
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Received a valid push on git.bioconductor.org; starting a build for commit id: a5f8e2dedc0736227c87e80154520a7158ec11ef |
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Dear Package contributor, This is the automated single package builder at bioconductor.org. Your package has been built on the Bioconductor Single Package Builder. On one or more platforms, the build results were: "ERROR". Please see the build report for more details. The following are build products from R CMD build on the Single Package Builder: Links above active for 21 days. Remember: if you submitted your package after July 7th, 2020, |
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Received a valid push on git.bioconductor.org; starting a build for commit id: bb58aa218d62d4e2c214a7f6fea380528bf993f8 |
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Dear Package contributor, This is the automated single package builder at bioconductor.org. Your package has been built on the Bioconductor Single Package Builder. On one or more platforms, the build results were: "ERROR". Please see the build report for more details. The following are build products from R CMD build on the Single Package Builder: Links above active for 21 days. Remember: if you submitted your package after July 7th, 2020, |
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Received a valid push on git.bioconductor.org; starting a build for commit id: 880a28b24136f0efbccc93d195963014d07f1944 |
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Dear Package contributor, This is the automated single package builder at bioconductor.org. Your package has been built on the Bioconductor Single Package Builder. On one or more platforms, the build results were: "ERROR". Please see the build report for more details. The following are build products from R CMD build on the Single Package Builder: Links above active for 21 days. Remember: if you submitted your package after July 7th, 2020, |
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Received a valid push on git.bioconductor.org; starting a build for commit id: 87262970863fad38a96e57b99690747574d314fd |
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Dear Package contributor, This is the automated single package builder at bioconductor.org. Your package has been built on the Bioconductor Single Package Builder. Congratulations! The package built without errors or warnings Please see the build report for more details. The following are build products from R CMD build on the Single Package Builder: Links above active for 21 days. Remember: if you submitted your package after July 7th, 2020, |
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