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sciCNV
Update the following URL to point to the GitHub repository of the package you wish to submit to Bioconductor
- Repository: https://github.com/alimahdipour/sciCNV
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Hi @alimahdipour
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: sciCNV
Title: sciCNV
Version: 0.99.0
Authors@R:
person("Ali","Mahdipour-Shirayeh", email = "[email protected]", role = "cre", comment = c(ORCID = "0000-0002-4201-2937"))
Description: The sciCNV pipeline enables profiling of RNA and DNA copy number in the same cells, and thus permits direct examination of the influence of genomic CNV on gene expression and cellular programs to capture intra-tumor heterogeneity.
License: use_mit_license()
Encoding: UTF-8
LazyData: true
Roxygen: list(markdown = TRUE)
RoxygenNote: 7.1.2
biocViews: CopyNumberVariation, RNASeq, GeneExpression, SingleCell, GenomicVariation, Clustering
Imports:
devtools,
base,
dplyr,
Matrix,
qlcMatrix,
svd,
ggplot2,
ggridges,
viridis,
scales,
umap,
parallel
VignetteBuilder: knitr
Suggests:
rmarkdown,
knitr
A reviewer has been assigned to your package. Learn what to expect during the review process.
IMPORTANT: Please read this documentation for setting up remotes to push to git.bioconductor.org. It is required to push a version bump to git.bioconductor.org to trigger a new build.
Bioconductor utilized your github ssh-keys for git.bioconductor.org access. To manage keys and future access you may want to active your Bioconductor Git Credentials Account
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". 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
[email protected]:packages/sciCNV to trigger a new build.
A quick tutorial for setting up remotes and pushing to upstream can be found here.
I tried to follow the instructions and to push changes to [email protected]:packages/sciCNV for a new build by bumping the package version from 0.99.0 to 0.99.1. However, did not receive any notification if it is going to be built. How does this work?
We don't see changes pushed to git.bioconductor.org. Can you provide more information like showing the results of git remote -v and the command and full results of what is shown when trying to push
Here is the result of trying that:
origin [email protected]:alimahdipour/sciCNV.git (fetch)
origin [email protected]:alimahdipour/sciCNV.git (push)
upsream [email protected]:packages/sciCNV (fetch)
upsream [email protected]:packages/sciCNV (push)
upstream [email protected]:packages/sciCNV (fetch)
upstream [email protected]:packages/sciCNV (push)
Then I tried git fetch --al with this result:
Fetching origin
Fetching upstream
Fetching upsream
also tried git merge upsream/master but I think it has not been performed properly:
error: Your local changes to the following files would be overwritten by merge:
R/CNV_htmp_glist.R
R/CNV_htmp_gloc.R
R/Mito_umi_gn.R
man/CNV_htmp_glist.Rd
man/CNV_htmp_gloc.Rd
man/CNV_infer.Rd
man/CNV_score.Rd
man/Mito_umi_gn.Rd
man/Opt_MeanSD_RTAM1.Rd
man/Opt_MeanSD_RTAM2.Rd
man/RTAM_normalization.Rd
man/Scaling_CNV.Rd
man/Sketch_AveCNV.Rd
man/heatmap_break_glist.Rd
man/heatmap_break_gloc.Rd
man/sciCNV.Rd
Please commit your changes or stash them before you merge.
Aborting
Please see the advise of the ERROR message. It appears you have changes you have not yet committed in your local repository
Hi @Ishep
I tried to commit changes using git pull and git stash but all my updated files were gone and I had to redo all changes. Now when I try git fetch --all it shows error:
Fetching origin
error: refs/remotes/origin/R-codes does not point to a valid object!
error: refs/remotes/origin/alimahdipour-patch-1 does not point to a valid object!
error: refs/remotes/origin/alimahdipour-patch-2 does not point to a valid object!
error: refs/remotes/origin/sciCNV/Figures/Fig1 does not point to a valid object!
error: refs/remotes/origin/sciCNV_function does not point to a valid object!
error: refs/remotes/origin/R-codes does not point to a valid object!
error: refs/remotes/origin/alimahdipour-patch-1 does not point to a valid object!
error: refs/remotes/origin/alimahdipour-patch-2 does not point to a valid object!
error: refs/remotes/origin/sciCNV/Figures/Fig1 does not point to a valid object!
error: refs/remotes/origin/sciCNV_function does not point to a valid object!
error: refs/remotes/origin/R-codes does not point to a valid object!
error: refs/remotes/origin/alimahdipour-patch-1 does not point to a valid object!
error: refs/remotes/origin/alimahdipour-patch-2 does not point to a valid object!
error: refs/remotes/origin/sciCNV/Figures/Fig1 does not point to a valid object!
error: refs/remotes/origin/sciCNV_function does not point to a valid object!
error: Could not read 380e8c4087d0d26192457f6431ea6c67e459e5d4
error: Could not read 791bd748e95665aa598a5cb41bc1f431c95113c5
error: refs/remotes/origin/R-codes does not point to a valid object!
error: refs/remotes/origin/alimahdipour-patch-1 does not point to a valid object!
error: refs/remotes/origin/alimahdipour-patch-2 does not point to a valid object!
error: refs/remotes/origin/sciCNV/Figures/Fig1 does not point to a valid object!
error: refs/remotes/origin/sciCNV_function does not point to a valid object!
error: Could not read 5b9ae24a2c2e9108acda1e17fb1e9bb291f4b189
error: Could not read 33c49334882ec13b9b147ee1333a51c3c126f5ce
remote: Enumerating objects: 93, done.
remote: Counting objects: 100% (93/93), done.
remote: Compressing objects: 100% (60/60), done.
remote: Total 60 (delta 43), reused 0 (delta 0), pack-reused 0
Unpacking objects: 100% (60/60), done.
fatal: unresolved deltas left after unpacking
fatal: unpack-objects failed
error: Could not fetch origin
Fetching upstream
error: refs/remotes/origin/R-codes does not point to a valid object!
error: refs/remotes/origin/alimahdipour-patch-1 does not point to a valid object!
...
It seems that my Github remote is broken. Please any idea how to fix it?
Dear @alimahdipour ,
We have reopened the issue to continue the review process. Please remember to push a version bump to git.bioconductor.org to trigger a new build.
Received a valid push on git.bioconductor.org; starting a build for commit id: 2ed0ba1e1d1b53fdd1cc4f0d7bfe10897cd8965e
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. 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
[email protected]:packages/sciCNV to trigger a new build.
A quick tutorial for setting up remotes and pushing to upstream can be found here.
Please note all dependencies need to be active on CRAN or Bioconductor. GMD has not been in CRAN since 2018. It will need to be removed as a package dependency.
Thanks for the comment, I removed the GMD package and added the R function as needed in the package. Hope all are good now; now trying to push changes to [email protected]:packages/sciCNV.
Received a valid push on git.bioconductor.org; starting a build for commit id: 5e196d845dee70d4537bea6ca8e951dce55e577a
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
[email protected]:packages/sciCNV 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: 756c04222db88bca402016b713512546a6dcc58b
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
[email protected]:packages/sciCNV 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: 196fdb7583aa6da39f1302db1cd2a3e25034417f
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
[email protected]:packages/sciCNV 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: e1025e19d9931d609296a9c8e225d81cff8db8e1
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
[email protected]:packages/sciCNV 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: 621bbefac650411fdbf31dce7f5f12cec2a4b2cd
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
[email protected]:packages/sciCNV 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: ea3e3514ee39c18c46b86d830b4f69662e223d1a
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
[email protected]:packages/sciCNV 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: f9e74f90850cfeaf4ff4d4dd7bfce2fa905d0dfd
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
[email protected]:packages/sciCNV 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: 4b7ddfe45749b464ed2a44802ce96b221483a194
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
[email protected]:packages/sciCNV 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: beaa6cc97e282b855907d7976ee41e07cde559a7