error CytoML

[yrong-2]

Hi RGLab team, I keep hitting error when trying to install CytoML on R

This is the latest error when I typed library("CytoML")

Error: package or namespace load failed for ‘CytoML’: object ‘getCompensationObj’ is not exported by 'namespace:flowWorkspace'

Can you please help? Thanks

[SamGG]

SessionInfo() please.

[yrong-2]

sessionInfo()

R version 3.6.3 (2020-02-29) Platform: x86_64-apple-darwin15.6.0 (64-bit) Running under: macOS Mojave 10.14.6

Matrix products: default BLAS: /System/Library/Frameworks/Accelerate.framework/Versions/A/Frameworks/vecLib.framework/Versions/A/libBLAS.dylib LAPACK: /Library/Frameworks/R.framework/Versions/3.6/Resources/lib/libRlapack.dylib

Random number generation: RNG: Mersenne-Twister Normal: Inversion Sample: Rounding

locale: [1] en_AU.UTF-8/en_AU.UTF-8/en_AU.UTF-8/C/en_AU.UTF-8/en_AU.UTF-8

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

other attached packages: [1] forcats_0.5.0 stringr_1.4.0 dplyr_0.8.5
[4] purrr_0.3.3 readr_1.3.1 tidyr_1.0.2
[7] tibble_3.0.0 ggplot2_3.3.0 tidyverse_1.3.0.9000 [10] flowStats_3.45.5 flowViz_1.50.0 lattice_0.20-40
[13] flowCore_1.52.1 githubinstall_0.2.2 flowWorkspace_3.34.1

loaded via a namespace (and not attached): [1] nlme_3.1-145 ncdfFlow_2.32.0 matrixStats_0.56.0 [4] fs_1.4.0 usethis_1.5.1 lubridate_1.7.4
[7] devtools_2.2.2 RColorBrewer_1.1-2 httr_1.4.1
[10] rprojroot_1.3-2 Rgraphviz_2.30.0 tools_3.6.3
[13] backports_1.1.5 R6_2.4.1 KernSmooth_2.23-16 [16] DBI_1.1.0 BiocGenerics_0.32.0 colorspace_1.4-1
[19] withr_2.1.2 tidyselect_1.0.0 gridExtra_2.3
[22] prettyunits_1.1.1 processx_3.4.2 curl_4.3
[25] compiler_3.6.3 rvest_0.3.5 graph_1.64.0
[28] cli_2.0.2.9000 Biobase_2.46.0 xml2_1.2.5
[31] desc_1.2.0 scales_1.1.0 DEoptimR_1.0-8
[34] hexbin_1.28.1 mvtnorm_1.1-0 robustbase_0.93-6
[37] callr_3.4.3 RBGL_1.62.1 digest_0.6.25
[40] rrcov_1.5-2 base64enc_0.1-3 jpeg_0.1-8.1
[43] pkgconfig_2.0.3 sessioninfo_1.1.1 dbplyr_1.4.2
[46] readxl_1.3.1 rlang_0.4.5 rstudioapi_0.11
[49] generics_0.0.2 jsonlite_1.6.1 mclust_5.4.5
[52] magrittr_1.5 Matrix_1.2-18 Rcpp_1.0.4
[55] munsell_0.5.0 fansi_0.4.1 lifecycle_0.2.0
[58] stringi_1.4.6 yaml_2.2.1 MASS_7.3-51.5
[61] zlibbioc_1.32.0 pkgbuild_1.0.6 grid_3.6.3
[64] parallel_3.6.3 crayon_1.3.4 haven_2.2.0
[67] splines_3.6.3 hms_0.5.3 ps_1.3.2
[70] pillar_1.4.3 RUnit_0.4.32 fda_2.4.8.1
[73] corpcor_1.6.9 stats4_3.6.3 pkgload_1.0.2
[76] reprex_0.3.0 XML_3.99-0.3 glue_1.3.2
[79] latticeExtra_0.6-29 modelr_0.1.6 data.table_1.12.8
[82] remotes_2.1.1 RcppParallel_5.0.0 png_0.1-7
[85] vctrs_0.2.4 cellranger_1.1.0 testthat_2.3.2
[88] gtable_0.3.0 assertthat_0.2.1 ks_1.11.7
[91] broom_0.5.5 flowUtils_1.49.2 IDPmisc_1.1.20
[94] pcaPP_1.9-73 memoise_1.1.0 cluster_2.1.0
[97] ellipsis_0.3.0

[yrong-2]

Could the error be due to my upgrade to the latest version of the R?

[SamGG]

Being nor the developper nor under Mac, I can't help you now. The team has a huge work currently in order to go with R 4.0. I think R 3.6.3 should be OK, and you have the right version of flowworkspace as mentioned on Bioconductor. You could either wait for an answer from them in a few hours, either look at open and closed issues mentionning flowworkspace. Best.

[yrong-2]

Thanks Sam. No worries, I'll continue working on it and see if I can solve it.

[SamGG]

I could tell you switch to the devel version of Bioconductor aka 3.11, but it could be risky. I think R 3.6.3 should be OK. The best option should be to reinstall flowworkpace. I didn't see any import of getCompensationObj in CytoML's NAMESPACE. Good luck!

[yrong-2]

I managed to install CytoML by re-installing R 3.6.1.