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bvieth / powsimR

Power analysis is essential to optimize the design of RNA-seq experiments and to assess and compare the power to detect differentially expressed genes. PowsimR is a flexible tool to simulate and evaluate differential expression from bulk and especially single-cell RNA-seq data making it suitable for a priori and posterior power analyses.
https://bvieth.github.io/powsimR/
Artistic License 2.0
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Installation Issue #46

Closed K-Ramachandra-Murthy closed 4 years ago

K-Ramachandra-Murthy commented 4 years ago

Hi, I am trying to install "powsimR" in R version 4.0.0. But I am encountering the following error. Can you please help me to resolve the issue.

devtools::install_github("bvieth/powsimR", build_vignettes = TRUE, dependencies = FALSE) Downloading GitHub repo bvieth/powsimR@master √ checking for file 'C:\Users\DrKRa\AppData\Local\Temp\Rtmpkvz7Mf\remotes3b2c2bb37131\bvieth-powsimR-dcbe954/DESCRIPTION' ...

  • preparing 'powsimR': (1.1s) √ checking DESCRIPTION meta-information ...

  • installing the package to build vignettes

  • installing source package 'powsimR' ... using staged installation R ** data * moving datasets to lazyload DB inst ** byte-compile and prepare package for lazy loading Warning: replacing previous import 'DECENT::lrTest' by 'MAST::lrTest' when loading 'powsimR' Error: object 'zlm.SingleCellAssay' is not exported by 'namespace:MAST' Execution halted ERROR: lazy loading failed for package 'powsimR'

  • removing 'C:/Users/DrKRa/AppData/Local/Temp/Rtmp6BoTWK/Rinst411473b81ffc/powsimR'

    ERROR: package installation failed Error: Failed to install 'powsimR' from GitHub: System command 'Rcmd.exe' failed, exit status: 1, stdout + stderr (last 10 lines): E> * moving datasets to lazyload DB E> inst E> * byte-compile and prepare package for lazy loading E> Warning: replacing previous import 'DECENT::lrTest' by 'MAST::lrTest' when loading 'powsimR' E> Error: object 'zlm.SingleCellAssay' is not exported by 'namespace:MAST' E> Execution halted E> ERROR: lazy loading failed for package 'powsimR' E> removing 'C:/Users/DrKRa/AppData/Local/Temp/Rtmp6BoTWK/Rinst411473b81ffc/powsimR' E> ----------------------------------- E> ERROR: package installation failed

Thanks Ramachandra

GerardTromp commented 4 years ago

I second this problem. It seems that either MAST has changed or some other change in NAMESPACE rules causes the reliance on zlm.SingleCellAssay to become a problem.

Currently: 'zlm.SingleCellAssay' is not exported by 'namespace:MAST'

GerardTromp commented 4 years ago

Indeed MAST states that zlm.SingleCellAssay is defunct. Since version 1.5.3 Transition to use SingleCellExperiment and manage log counts slot.

And in the Readme: New Features and announcements MAST has been ported to use SingleCellExperiment under the hood, and is in Bioconductor. We now make an effort to track assay contents (counts vs log counts). This should facilitate interaction with Scater and SCRAN.

GerardTromp commented 4 years ago

OK. This problem can be solved by editing R/utlis_DEdetection.R and removing the .SingleCellAssay from zlm. Also update the NAMESPACE file with the same edit.

It next produces an error in scater Error: object 'calcAverage' is not exported by 'namespace:scater'

GerardTromp commented 4 years ago

OK, so the calcAverage not exported by namespace:scater is solved by changing the powsimR code in R/utils_estimate.R and in NAMESPACE to reflect the change in scater where the class was renamed to calculateAverage.

After these two changes, the package compiles as of 2020-05-13. Now to test if there are any hidden hiccups.

K-Ramachandra-Murthy commented 4 years ago

Hi Gerard Tromp, After making the suggested changes, it complied without any errors. Thank you. Appreciate your help.

Ramachandra

GerardTromp commented 4 years ago

My pleasure,

I have also contacted the package author with the relevant changes.

Although MAST had the information in the NEWS and Readme, in scater it was a silent change. Silent changes are very annoying.

Gerard Gerard Tromp, PhD Professor and Research Chair in Bioinformatics SAMRC-SHIP South African Tuberculosis Bioinformatics Initiative (SATBBI) Centre for Bioinformatics and Computational Biology DST/NRF Centre of Excellence for Biomedical Tuberculosis Research SAMRC Center for Molecular and Cellular Biology Division of Molecular Biology and Human Genetics Department of Biomedical Sciences Faculty of Medicine and Health Sciences Stellenbosch University Tygerberg, 7505, South Africa +27-21-938-9947 Home Page: https://goo.gl/CaXRR Publications: https://goo.gl/SwwxM5 Google Scholar: https://goo.gl/NAaET [cid:image001.png@01D62946.84C30070]

From: K-Ramachandra-Murthy Sent: Wednesday, May 13, 2020 16:46 To: bvieth/powsimR powsimR@noreply.github.com Cc: Tromp, Gerard, Prof [gctromp@sun.ac.za] gctromp@sun.ac.za; Comment comment@noreply.github.com Subject: Re: [bvieth/powsimR] Installation Issue (#46)

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Hi Gerard Tromp, After making the suggested changes, it complied without any errors. Thank you. Appreciate your help.

Ramachandra

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bvieth commented 4 years ago

Hello,

I am sorry that you have encountered this issue. I have updated powsimR to be compatible with the newest Bioconductor release (MAST and scater had some name changes of functions and DEDS is deprecated). I hope you will give it another go.

Feel free to contact me again.

Best Beate