unable to install and run cytofclean on my dataset

[Hesam1378]

library("cytofclean")
Error in library("cytofclean") : there is no package called ‘cytofclean’

cytofclean_GUI()
Error in cytofclean_GUI() : could not find function "cytofclean_GUI"

[JimboMahoney]

Hi Hesam,

Thanks - I've had some reports from some users that it doesn't install properly, but others it works fine, so we need to do some digging to find out why / what's different.

Here's some things to try:

1. Maybe it's the same problem as described here?

2. Can you do sessionInfo() and copy/paste what it outputs?

[Hesam1378]

Hi James, Thank you! I will try the solutions on https://stackoverflow.com/ Here is the output:

sessionInfo()

R version 3.6.3 (2020-02-29) Platform: x86_64-w64-mingw32/x64 (64-bit) Running under: Windows 10 x64 (build 18362) Matrix products: default locale: [1] LC_COLLATE=English_United States.1252 [2] LC_CTYPE=English_United States.1252 [3] LC_MONETARY=English_United States.1252 [4] LC_NUMERIC=C [5] LC_TIME=English_United States.1252 attached base packages: [1] stats graphics grDevices utils datasets [6] methods base loaded via a namespace (and not attached): [1] compiler_3.6.3 tools_3.6.3

Best, Hesam Hesam Movassagh, Ph.D. Postdoctoral Fellow Sean N. Parker Center for Allergy & Asthma Research Stanford University School of Medicine Grant Building, S314 300 Pasteur Dr. Stanford, CA 94305

…

________________________________ From: James <notifications@github.com> Sent: Tuesday, March 24, 2020 12:01 AM To: JimboMahoney/cytofclean <cytofclean@noreply.github.com> Cc: Hesam Movassagh <hesamov@stanford.edu>; Author <author@noreply.github.com> Subject: Re: [JimboMahoney/cytofclean] unable to install and run cytofclean on my dataset (#12) Hi Hesam, Thanks - I've had some reports from some users that it doesn't install properly, but others it works fine, so we need to do some digging to find out why / what's different. Here's some things to try: 1. Maybe it's the same problem as described here<https://stackoverflow.com/questions/19407092/r-not-finding-package-even-after-package-installation>? 2. Can you do sessionInfo() and copy/paste what it outputs? — You are receiving this because you authored the thread. Reply to this email directly, view it on GitHub<#12 (comment)>, or unsubscribe<https://github.com/notifications/unsubscribe-auth/AMM27JYEN3AP5D4RRV7UMLLRJBLDPANCNFSM4LSI46BQ>.

[JimboMahoney]

Just checking - have you also run the install commands?

if(!require(devtools)){
  install.packages("devtools") # If not already installed
}

if(!require(cytofclean)){
  devtools::install_github("JimboMahoney/cytofclean", dependencies = TRUE)
}

[Hesam1378]

Yes I have. On Mar 25, 2020, at 1:04 AM, James <notifications@github.com> wrote:  Just checking - have you also run the install commands? if(!require(devtools)){ install.packages("devtools") # If not already installed } if(!require(cytofclean)){ devtools::install_github("JimboMahoney/cytofclean", dependencies = TRUE) } — You are receiving this because you authored the thread. Reply to this email directly, view it on GitHub<#12 (comment)>, or unsubscribe<https://github.com/notifications/unsubscribe-auth/AMM27J3UFVI64G5P7ECY6STRJG3IZANCNFSM4LSI46BQ>.

[mflookp]

Hi,

when I try to install your package, this part of the code:

if(!require(cytofclean)){
devtools::install_github("JimboMahoney/cytofclean", dependencies = TRUE)
}

Returns this error:
The downloaded source packages are in
‘C:\Users\USER\AppData\Local\Temp\RtmpSU2bJh\downloaded_packages’
√ checking for file 'C:\Users\USER\AppData\Local\Temp\RtmpSU2bJh\remotes4db020b02e5b\JimboMahoney-cytofclean-5d22ed6/DESCRIPTION' (434ms)

• preparing 'cytofclean':
  E checking DESCRIPTION meta-information ...
  Malformed maintainer field.

  See section 'The DESCRIPTION file' in the 'Writing R Extensions'
  manual.

Error: Failed to install 'cytofclean' from GitHub:
System command 'Rcmd.exe' failed, exit status: 1, stdout + stderr:
E> * checking for file 'C:\Users\USER\AppData\Local\Temp\RtmpSU2bJh\remotes4db020b02e5b\JimboMahoney-cytofclean-5d22ed6/DESCRIPTION' ... OK
E> * preparing 'cytofclean':
E> * checking DESCRIPTION meta-information ... ERROR
E> Malformed maintainer field.
E>
E> See section 'The DESCRIPTION file' in the 'Writing R Extensions'
E> manual.
E>
Además: Warning messages:
1: In library(package, lib.loc = lib.loc, character.only = TRUE, logical.return = TRUE, :
there is no package called ‘cytofclean’
2: In file.copy(savedcopy, lib, recursive = TRUE) :
problema al copiar C:\Users\USER\Documents\R\win-library\4.0\00LOCK\colorspace\libs\x64\colorspace.dll a C:\Users\USER\Documents\R\win-library\4.0\colorspace\libs\x64\colorspace.dll: Permission denied

My output for sessionInfo():
R version 4.0.3 (2020-10-10)
Platform: x86_64-w64-mingw32/x64 (64-bit)
Running under: Windows 10 x64 (build 19043)

Matrix products: default

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

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

other attached packages:
[1] devtools_2.4.2 usethis_2.0.1

loaded via a namespace (and not attached):
[1] ncdfFlow_2.36.0 tsne_0.1-3 matrixStats_0.59.0
[4] fs_1.5.0 RColorBrewer_1.1-2 httr_1.4.2
[7] rprojroot_2.0.2 Rgraphviz_2.34.0 tools_4.0.3
[10] utf8_1.2.1 R6_2.5.0 uwot_0.1.10
[13] BiocGenerics_0.36.1 colorspace_2.0-1 flowWorkspace_4.2.0
[16] withr_2.4.2 prettyunits_1.1.1 tidyselect_1.1.1
[19] gridExtra_2.3 processx_3.5.2 curl_4.3.2
[22] compiler_4.0.3 graph_1.68.0 cli_3.0.0
[25] Biobase_2.50.0 xml2_1.3.2 ggcyto_1.18.0
[28] desc_1.3.0 scales_1.1.1 hexbin_1.28.2
[31] callr_3.7.0 RBGL_1.66.0 stringr_1.4.0
[34] digest_0.6.27 rmarkdown_2.9 base64enc_0.1-3
[37] dichromat_2.0-0 jpeg_0.1-8.1 pkgconfig_2.0.3
[40] htmltools_0.5.1.1 sessioninfo_1.1.1 changepoint_2.2.2
[43] fastmap_1.1.0 maps_3.3.0 rlang_0.4.11
[46] rstudioapi_0.13 pals_1.7 flowCore_2.2.0
[49] generics_0.1.0 zoo_1.8-9 jsonlite_1.7.2
[52] dplyr_1.0.7 magrittr_2.0.1 RProtoBufLib_2.2.0
[55] Matrix_1.2-18 Rcpp_1.0.6 munsell_0.5.0
[58] S4Vectors_0.28.1 fansi_0.5.0 lifecycle_1.0.0
[61] stringi_1.5.3 yaml_2.2.1 zlibbioc_1.36.0
[64] pkgbuild_1.2.0 plyr_1.8.6 grid_4.0.3
[67] parallel_4.0.3 crayon_1.4.1 lattice_0.20-41
[70] mapproj_1.2.7 knitr_1.33 ps_1.6.0
[73] pillar_1.6.1 igraph_1.2.6 pkgload_1.2.1
[76] reshape2_1.4.4 stats4_4.0.3 XML_3.99-0.6
[79] glue_1.4.2 evaluate_0.14 latticeExtra_0.6-29
[82] remotes_2.4.0 data.table_1.14.0 RcppParallel_5.1.4
[85] png_0.1-7 vctrs_0.3.8 testthat_3.0.3
[88] gtable_0.3.0 aws.s3_0.3.21 purrr_0.3.4
[91] cachem_1.0.5 ggplot2_3.3.5 xfun_0.24
[94] ConsensusClusterPlus_1.54.0 tibble_3.1.2 flowAI_1.20.1
[97] FlowSOM_1.22.0 cytolib_2.2.1 aws.signature_0.6.0
[100] tinytex_0.32 memoise_2.0.0 cluster_2.1.0
[103] CytoML_2.2.2 ellipsis_0.3.2

[JimboMahoney]

Hi,

when I try to install your package, this part of the code:

if(!require(cytofclean)){
devtools::install_github("JimboMahoney/cytofclean", dependencies = TRUE)
}

Returns this error:
The downloaded source packages are in
‘C:\Users\USER\AppData\Local\Temp\RtmpSU2bJh\downloaded_packages’
√ checking for file 'C:\Users\USER\AppData\Local\Temp\RtmpSU2bJh\remotes4db020b02e5b\JimboMahoney-cytofclean-5d22ed6/DESCRIPTION' (434ms)

• preparing 'cytofclean':
  E checking DESCRIPTION meta-information ...
  Malformed maintainer field.
  See section 'The DESCRIPTION file' in the 'Writing R Extensions'
  manual.

@mflookp - OK, this is because the maintainer field needed an e-mail address, which I have added.

If you clear your local copy, if it still exists, and try again?

[mflookp]

Hi,
when I try to install your package, this part of the code:
if(!require(cytofclean)){
devtools::install_github("JimboMahoney/cytofclean", dependencies = TRUE)
}
Returns this error:
The downloaded source packages are in
‘C:\Users\USER\AppData\Local\Temp\RtmpSU2bJh\downloaded_packages’
√ checking for file 'C:\Users\USER\AppData\Local\Temp\RtmpSU2bJh\remotes4db020b02e5b\JimboMahoney-cytofclean-5d22ed6/DESCRIPTION' (434ms)

• preparing 'cytofclean':
  E checking DESCRIPTION meta-information ...
  Malformed maintainer field.
  See section 'The DESCRIPTION file' in the 'Writing R Extensions'
  manual.

@mflookp - OK, this is because the maintainer field needed an e-mail address, which I have added.

If you clear your local copy, if it still exists, and try again?

Yes, it worked, thank you!