Re: [Bioc-devel] muleaData problems reported in the Build/check report for BioC 3.19 experimental data

2024-03-20 Thread Eszter Ari 
Hi Mike,

Many thanks!

Does this:
"Please take the time to address this by committing and pushing
changes to your package at git.bioconductor.org"
mean that I have to push it to the devel branch like this?

Is this mean that I have to push the changes to the devel branch of the
# to connect with the bioC repo - need to be done only once
git remote add upstream g...@git.bioconductor.org:packages/muleaData.git

# after every update in the main repo that we want to push to the
upstream/devel branch of BioC
git fetch --all
# change to the main branch
git checkout main
git merge origin/main
# change to the devel branch
git checkout devel
git merge main
git push upstream devel
# change back to the main branch
git checkout main

Best,
Eszter

On Wed, 20 Mar 2024 at 10:07, Mike Smith  wrote:

> Hi Eszter,
>
> If you're using ExperimentHub in your vignette then you need to add that
> to the Suggests field in your DESCRIPTION file.
>
> The R CMD check output you linked to mentions a similar issue for the code
> in your examples:
>
> * checking for unstated dependencies in examples ... WARNING
> '::' or ':::' imports not declared from:
>   ‘ExperimentHub’ ‘dplyr’
> 'library' or 'require' calls not declared from:
>   ‘ExperimentHub’ ‘dplyr’
>
> That should also be fixed by putting those packages in Suggests.
>
> Cheers,
> Mike
>
> On Wed, 20 Mar 2024 at 09:54, Eszter Ari  wrote:
>
>> Hi,
>>
>> I have a question a problem reported in the Build/check report for BioC
>> 3.19 experimental data:
>> I have created an experimental data package:
>> https://github.com/ELTEbioinformatics/muleaData
>> I have got this message from
>> bbs-nore...@bioconductor.org:
>> According to the Build/check report for BioC 3.19 experimental data,
>> the muleaData package has the following problem(s):  o ERROR for 'R CMD
>> check' on nebbiolo1. See the details here:
>>
>>
>> https://master.bioconductor.org/checkResults/3.19/data-experiment-LATEST/muleaData/nebbiolo1-checksrc.htmlAs
>> I see on the link there is a problem with the muleaData.Rmd file.
>> Previously I have been asked by @lshepherd
>>  to make the 'install' R
>> code chunk to eval=FALSE:
>>
>> https://github.com/Bioconductor/Contributions/issues/3291#issuecomment-1978971419
>>
>> ```{r 'install', eval=FALSE}
>> if (!require("BiocManager", quietly = TRUE))
>> install.packages("BiocManager")
>>
>> BiocManager::install("ExperimentHub")
>> BiocManager::install("muleaData")
>> ```
>>
>> Then the next 'example' chunk cannot be run:
>>
>> ```{r 'example'}
>>
>> # Calling the ExperimentHub library.
>> library(ExperimentHub)
>>
>> # Downloading the metadata from ExperimentHub.
>> eh <- ExperimentHub()
>>
>> # Creating the muleaData variable.
>> muleaData <- query(eh, "muleaData")
>>
>> # Checking the muleaData variable.
>> muleaData
>>
>> # Looking for the ExperimentalHub ID of i.e. target genes of transcription
>> # factors from TFLink in Caenorhabditis elegans.
>> mcols(muleaData) %>%
>> as.data.frame() %>%
>> dplyr::filter(species == "Caenorhabditis elegans" &
>> sourceurl == "https://tflink.net/;)
>>
>> # Creating a variable for the GMT data.frame of EH8735.
>> # EH8735 contains small-scale measurement results, where the target genes
>> are
>> # coded with Ensembl ID-s
>> Transcription_factor_TFLink_Caenorhabditis_elegans_SS_EnsemblID <-
>> muleaData[["EH8735"]]
>> ```
>>
>> *Should I change to eval=FALSE this chunk as well? *
>>
>> Ari, Eszter, habil, PhD
>> ariesz...@gmail.com +36 (70) 380 9833
>> postdoctoral researcher at *Synthetic and Systems Biology Unit, Biological
>> Research Centre, ELKH, Szeged, Hungary*
>> assistant professor at *Dep. Genetics, Eötvös Loránd University, Budapest,
>> Hungary*
>>
>> [[alternative HTML version deleted]]
>>
>> ___
>> Bioc-devel@r-project.org mailing list
>> https://stat.ethz.ch/mailman/listinfo/bioc-devel
>>
>

-- 
Ari, Eszter, habil, PhD
ariesz...@gmail.com +36 (70) 380 9833
postdoctoral researcher at *Synthetic and Systems Biology Unit, Biological
Research Centre, ELKH, Szeged, Hungary*
assistant professor at *Dep. Genetics, Eötvös Loránd University, Budapest,
Hungary*

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Re: [Bioc-devel] muleaData problems reported in the Build/check report for BioC 3.19 experimental data

2024-03-20 Thread Mike Smith 
Hi Eszter,

If you're using ExperimentHub in your vignette then you need to add that to
the Suggests field in your DESCRIPTION file.

The R CMD check output you linked to mentions a similar issue for the code
in your examples:

* checking for unstated dependencies in examples ... WARNING
'::' or ':::' imports not declared from:
  ‘ExperimentHub’ ‘dplyr’
'library' or 'require' calls not declared from:
  ‘ExperimentHub’ ‘dplyr’

That should also be fixed by putting those packages in Suggests.

Cheers,
Mike

On Wed, 20 Mar 2024 at 09:54, Eszter Ari  wrote:

> Hi,
>
> I have a question a problem reported in the Build/check report for BioC
> 3.19 experimental data:
> I have created an experimental data package:
> https://github.com/ELTEbioinformatics/muleaData
> I have got this message from
> bbs-nore...@bioconductor.org:
> According to the Build/check report for BioC 3.19 experimental data,
> the muleaData package has the following problem(s):  o ERROR for 'R CMD
> check' on nebbiolo1. See the details here:
>
>
> https://master.bioconductor.org/checkResults/3.19/data-experiment-LATEST/muleaData/nebbiolo1-checksrc.htmlAs
> I see on the link there is a problem with the muleaData.Rmd file.
> Previously I have been asked by @lshepherd
>  to make the 'install' R
> code chunk to eval=FALSE:
>
> https://github.com/Bioconductor/Contributions/issues/3291#issuecomment-1978971419
>
> ```{r 'install', eval=FALSE}
> if (!require("BiocManager", quietly = TRUE))
> install.packages("BiocManager")
>
> BiocManager::install("ExperimentHub")
> BiocManager::install("muleaData")
> ```
>
> Then the next 'example' chunk cannot be run:
>
> ```{r 'example'}
>
> # Calling the ExperimentHub library.
> library(ExperimentHub)
>
> # Downloading the metadata from ExperimentHub.
> eh <- ExperimentHub()
>
> # Creating the muleaData variable.
> muleaData <- query(eh, "muleaData")
>
> # Checking the muleaData variable.
> muleaData
>
> # Looking for the ExperimentalHub ID of i.e. target genes of transcription
> # factors from TFLink in Caenorhabditis elegans.
> mcols(muleaData) %>%
> as.data.frame() %>%
> dplyr::filter(species == "Caenorhabditis elegans" &
> sourceurl == "https://tflink.net/;)
>
> # Creating a variable for the GMT data.frame of EH8735.
> # EH8735 contains small-scale measurement results, where the target genes
> are
> # coded with Ensembl ID-s
> Transcription_factor_TFLink_Caenorhabditis_elegans_SS_EnsemblID <-
> muleaData[["EH8735"]]
> ```
>
> *Should I change to eval=FALSE this chunk as well? *
>
> Ari, Eszter, habil, PhD
> ariesz...@gmail.com +36 (70) 380 9833
> postdoctoral researcher at *Synthetic and Systems Biology Unit, Biological
> Research Centre, ELKH, Szeged, Hungary*
> assistant professor at *Dep. Genetics, Eötvös Loránd University, Budapest,
> Hungary*
>
> [[alternative HTML version deleted]]
>
> ___
> Bioc-devel@r-project.org mailing list
> https://stat.ethz.ch/mailman/listinfo/bioc-devel
>

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[Bioc-devel] muleaData problems reported in the Build/check report for BioC 3.19 experimental data

2024-03-20 Thread Eszter Ari 
Hi,

I have a question a problem reported in the Build/check report for BioC
3.19 experimental data:
I have created an experimental data package:
https://github.com/ELTEbioinformatics/muleaData
I have got this message from
bbs-nore...@bioconductor.org:
According to the Build/check report for BioC 3.19 experimental data,
the muleaData package has the following problem(s):  o ERROR for 'R CMD
check' on nebbiolo1. See the details here:

https://master.bioconductor.org/checkResults/3.19/data-experiment-LATEST/muleaData/nebbiolo1-checksrc.htmlAs
I see on the link there is a problem with the muleaData.Rmd file.
Previously I have been asked by @lshepherd
 to make the 'install' R
code chunk to eval=FALSE:
https://github.com/Bioconductor/Contributions/issues/3291#issuecomment-1978971419

```{r 'install', eval=FALSE}
if (!require("BiocManager", quietly = TRUE))
install.packages("BiocManager")

BiocManager::install("ExperimentHub")
BiocManager::install("muleaData")
```

Then the next 'example' chunk cannot be run:

```{r 'example'}

# Calling the ExperimentHub library.
library(ExperimentHub)

# Downloading the metadata from ExperimentHub.
eh <- ExperimentHub()

# Creating the muleaData variable.
muleaData <- query(eh, "muleaData")

# Checking the muleaData variable.
muleaData

# Looking for the ExperimentalHub ID of i.e. target genes of transcription
# factors from TFLink in Caenorhabditis elegans.
mcols(muleaData) %>%
as.data.frame() %>%
dplyr::filter(species == "Caenorhabditis elegans" &
sourceurl == "https://tflink.net/;)

# Creating a variable for the GMT data.frame of EH8735.
# EH8735 contains small-scale measurement results, where the target genes are
# coded with Ensembl ID-s
Transcription_factor_TFLink_Caenorhabditis_elegans_SS_EnsemblID <-
muleaData[["EH8735"]]
```

*Should I change to eval=FALSE this chunk as well? *

Ari, Eszter, habil, PhD
ariesz...@gmail.com +36 (70) 380 9833
postdoctoral researcher at *Synthetic and Systems Biology Unit, Biological
Research Centre, ELKH, Szeged, Hungary*
assistant professor at *Dep. Genetics, Eötvös Loránd University, Budapest,
Hungary*

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