[Bioc-devel] msqrob2 0.99.3 valid push and build started but no build report

Lieven Clement L|even@C|ement @end|ng |rom UGent@be
Thu Apr 29 19:43:29 CEST 2021

Dear Nitesh,

My apologies for mailing you again.
I noticed that you are assigned to our msqrob2 package so I took the liberty to mail you directly.

I have pushed msqrob2 version 0.99.3 yesterday.
I received following message: "Received a valid push on git.bioconductor.org<http://git.bioconductor.org>; starting a build for commit id: 167129e2e63d0077079a1b16e2406eed1a5e950c"
But  I do not seem to get a build report.

With the latest version update msqrob2 0.99.3 I tried to address as many notes as possible so as to lighten the burden for your review.

However, I did not know how I had to address the warning in the bioconductor build of msqrob2 0.99.2
"Found the following significant warnings:
Warning: no function found corresponding to methods exports from 'S4Vectors' for: 'combineRows' "

This warning did not occur in the build of msqrob2 0.99.1. with dependency on R 4.0 while it does version 0.99.2 that included a dependency on R 4.1.

I checked all files in the R/ directory and the NAMESPACE file of the msqrob2 package and I do not seem to find where I use the combineRows function. I guess it is imported by one of the packages that msqrob2 depends upon, e.g. QFeatures and summarizedExperiment import from S4vectors.

 I also do not seem to have this warning on my system. (See sessionInfo below). On my system the R CMD checks run without warnings and notes and the BiocChecks also run without warnings nor errors and with 4 notes.

Thank you for handling our package,



R Under development (unstable) (2021-02-19 r80028)
Platform: x86_64-apple-darwin17.0 (64-bit)
Running under: macOS Catalina 10.15.7

Matrix products: default
BLAS:   /Library/Frameworks/R.framework/Versions/4.1/Resources/lib/libRblas.dylib
LAPACK: /Library/Frameworks/R.framework/Versions/4.1/Resources/lib/libRlapack.dylib

[1] C/UTF-8/C/C/C/C

attached base packages:
[1] parallel  stats4    stats     graphics  grDevices utils     datasets
[8] methods   base

other attached packages:
 [1] msqrob2_0.99.2               QFeatures_1.1.3
 [3] MultiAssayExperiment_1.17.13 SummarizedExperiment_1.21.1
 [5] Biobase_2.51.0               GenomicRanges_1.43.3
 [7] GenomeInfoDb_1.27.6          IRanges_2.25.6
 [9] S4Vectors_0.29.7             BiocGenerics_0.37.1
[11] MatrixGenerics_1.3.1         matrixStats_0.58.0

loaded via a namespace (and not attached):
 [1] nlme_3.1-152            ProtGenerics_1.23.7     bitops_1.0-6
 [4] fs_1.5.0                xopen_1.0.0             usethis_2.0.1
 [7] devtools_2.4.0          httr_1.4.2              rprojroot_2.0.2
[10] tools_4.1.0             utf8_1.1.4              R6_2.5.0
[13] lazyeval_0.2.2          withr_2.4.1             prettyunits_1.1.1
[16] processx_3.5.1          curl_4.3                compiler_4.1.0
[19] graph_1.69.0            cli_2.4.0               BiocCheck_1.27.13
[22] xml2_1.3.2              desc_1.3.0              DelayedArray_0.17.9
[25] callr_3.7.0             RBGL_1.67.0             digest_0.6.27
[28] commonmark_1.7          stringr_1.4.0           minqa_1.2.4
[31] stringdist_0.9.6.3      XVector_0.31.1          pkgconfig_2.0.3
[34] lme4_1.1-26             sessioninfo_1.1.1       fastmap_1.1.0
[37] limma_3.47.8            rlang_0.4.10            rstudioapi_0.13
[40] jsonlite_1.7.2          BiocParallel_1.25.4     RCurl_1.98-1.2
[43] magrittr_2.0.1          GenomeInfoDbData_1.2.4  Matrix_1.3-2
[46] Rcpp_1.0.6              fansi_0.4.2             MsCoreUtils_1.3.2
[49] lifecycle_1.0.0         stringi_1.5.3           MASS_7.3-53.1
[52] zlibbioc_1.37.0         pkgbuild_1.2.0          biocViews_1.59.3
[55] grid_4.1.0              crayon_1.4.1            lattice_0.20-41
[58] splines_4.1.0           knitr_1.31              ps_1.5.0
[61] pillar_1.5.0            optparse_1.6.6          RUnit_0.4.32
[64] boot_1.3-27             codetools_0.2-18        pkgload_1.2.1
[67] XML_3.99-0.5            glue_1.4.2              remotes_2.3.0
[70] BiocManager_1.30.10     vctrs_0.3.6             nloptr_1.2.2.2
[73] testthat_3.0.2          rcmdcheck_1.3.3         getopt_1.20.3
[76] purrr_0.3.4.9000        cachem_1.0.4            xfun_0.21
[79] AnnotationFilter_1.15.0 roxygen2_7.1.1          tibble_3.1.0
[82] memoise_2.0.0           statmod_1.4.35          ellipsis_0.3.1

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