Question

Cannot install and load MSstats package

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zz298 • 0

@zz298-15416

Last seen 6.6 years ago

Hi,

I have problem loading the MSstats package.

I followed the instructions to install the package but when I try to load, here is the error message I got:

> library('MSstats', warn.conflicts = F, quietly = T, verbose = F)
Error: package or namespace load failed for ‘MSstats’:
 object ‘warnErrList’ is not exported by 'namespace:utils'

Does anyone know what the problem may be?

Thanks a lot!

Bests,

ZZ

proteomics massspectrometry msstats • 1.8k views

ADD COMMENT • link updated 6.6 years ago by Laurent Gatto 1.6k • written 6.6 years ago by zz298 • 0

score 0 · Answer 1 · 2018-04-03

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Laurent Gatto 1.6k

@laurent-gatto-5645

Last seen 6 weeks ago

Belgium

1. It would be more useful if you could run library("MSstats") without limiting any messages.

2. What is your sessionInfo().

3. Could you confirm that you installed the package with BiocInstaller::biocLite("MSstats"). It might also help running BiocInstaller::biocLite() to make sure all packages are updated.

ADD COMMENT • link 6.6 years ago Laurent Gatto 1.6k

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Hi,

Thank you so much for your response!

1. I tried the commend without limitation, the feedback was the same.

2. The sessioninfo is as follow:

R version 3.4.4 (2018-03-15)
Platform: x86_64-w64-mingw32/x64 (64-bit)
Running under: Windows >= 8 x64 (build 9200)

Matrix products: default

locale:
[1] LC_COLLATE=English_United States.1252 LC_CTYPE=English_United States.1252 LC_MONETARY=English_United States.1252
[4] LC_NUMERIC=C LC_TIME=English_United States.1252

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

other attached packages:
[1] BiocInstaller_1.28.0 scales_0.5.0

loaded via a namespace (and not attached):
[1] Rcpp_0.12.16 pillar_1.2.1 compiler_3.4.4 plyr_1.8.4 bindr_0.1.1 iterators_1.0.9 tools_3.4.4
[8] tibble_1.4.2 nlme_3.1-131.1 gtable_0.2.0 lattice_0.20-35 pkgconfig_2.0.1 rlang_0.2.0 psych_1.8.3.3
[15] foreach_1.4.4 parallel_3.4.4 bindrcpp_0.2.2 dplyr_0.7.4 stringr_1.3.0 grid_3.4.4 glue_1.2.0
[22] R6_2.2.2 foreign_0.8-69 limma_3.34.9 tidyr_0.8.0 purrr_0.2.4 reshape2_1.4.3 ggplot2_2.2.1
[29] magrittr_1.5 splines_3.4.4 codetools_0.2-15 assertthat_0.2.0 mnormt_1.5-5 colorspace_1.3-2 stringi_1.1.7
[36] lazyeval_0.2.1 munsell_0.4.3 broom_0.4.4

3. I'm not sure if the installation is successful. It says the package is successfully unpacked. However, i cannot find the package on the list of packages in Rstudio. The packages should be up to date

ADD REPLY • link 6.6 years ago zz298 • 0

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And what happens when you type utils::warnErrList? If you get something like

Error: 'warnErrList' is not an exported object from 'namespace:utils'

could you try to reinstall utils with BiocInstaller::biocLite("utils") and try again to load MSstats.

ADD REPLY • link 6.6 years ago Laurent Gatto 1.6k

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hey , i had a similar problem while installing some CRAN packages (lsmeans).

I solved the problem by reinstalling nlme try this:

install.packages("nlme")

and then try loading your package

ADD REPLY • link 6.6 years ago k.dacca • 0