Issue with intallation Cytofkit2

[AGGAGGAGG]

Hello,

I tried to install cytofkit2 but I can't.

I have these Following lines:

devtools::install_github("JinmiaoChenLab/cytofkit2") Downloading GitHub repo JinmiaoChenLab/cytofkit2@master These packages have more recent versions available. Which would you like to update?

1: XML (3.98-1.18 -> 3.98-1.19) [CRAN]

Enter one or more numbers separated by spaces, or an empty line to cancel 1: 1 XML (3.98-1.18 -> 3.98-1.19) [CRAN] Installing 1 packages: XML

There is a binary version available but the source version is later: binary source needs_compilation XML 3.98-1.18 3.98-1.19 TRUE

installing the source package ‘XML’

trying URL 'https://cran.rstudio.com/src/contrib/XML_3.98-1.19.tar.gz' Content type 'application/x-gzip' length 1600788 bytes (1.5 MB) downloaded 1.5 MB

• installing source package 'XML' ... package 'XML' correctement décompressé et sommes MD5 vérifiées libs C:/RBuildTools/3.5/mingw_64/bin/gcc -I"C:/Users/aggou/Desktop/R-35~1.2/include" -DNDEBUG -I/include/libxml2 -I/include -DR=1 -DUSE_R=1 -DUSE_XML_VERSION_H=1 -DLIBXML -DUSE_EXTERNAL_SUBSET=1 -DROOT_HAS_DTD_NODE=1 -DUMP_WITH_ENCODING=1 -DXML_ELEMENT_ETYPE=1 -DXML_ATTRIBUTE_ATYPE=1 -DLIBXML2=1 -DHAVE_XML_HAS_FEATURE -DLIBXML_STATIC -O2 -Wall -std=gnu99 -mtune=generic -c DocParse.c -o DocParse.o In file included from DocParse.c:10:0: DocParse.h:18:27: fatal error: libxml/parser.h: No such file or directory

  include <libxml/parser.h>

                     ^

  compilation terminated. make: *** [C:/Users/aggou/Desktop/R-35~1.2/etc/x64/Makeconf:208: DocParse.o] Error 1 ERROR: compilation failed for package 'XML'

• removing 'C:/Users/aggou/Desktop/R-3.5.2/library/XML'
• restoring previous 'C:/Users/aggou/Desktop/R-3.5.2/library/XML' In R CMD INSTALL Error in i.p(...) : (converted from warning) installation of package ‘XML’ had non-zero exit status

Could you help me to fixe it?

Thanks Anne

[SamGG]

Hi Anne, I think you should better not update packages from source. Simply reply that you don't want to update the XML package, and this will probably work. Best.

[siuhongh]

I have this error message:

Error: (converted from warning) cannot remove prior installation of package ‘BiocParallel’

Would you please help? Thanks.

[SamGG]

Hi, This message tells you that this package is in use on your computer. When installing any package, it's better to start with an empty environment, meaning no data and no packages loaded. In fact, packages are automatically loaded if an object is depending on it. For example, a flowFrame is an object/concept of the flowCore package, thus flowCore is loaded if a flowFrame is defined is the environment/variables of the R session. Moreover, if you have multiple R/RStudio opened at the same, one of them could use and lock a package (or a dependency) you want to update. So for installing a package, you should at least "Restart R" from the "Session" menu of RStudio. This should allow you to install packages and preserving your data. But I prefer to close ALL my RStudio projects and sessions, reopen RStudio, start a new empty project (new directory but not opening a new session) and then install whatever I need. HTH

[jinmiaochen]

Many thanks to Samuel for helping us!

[CNicholasMDA]

• installing source package ‘data.table’ ... package ‘data.table’ successfully unpacked and MD5 sums checked libs clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/usr/local/include -fopenmp -fPIC -Wall -g -O2 -c assign.c -o assign.o clang: error: unsupported option '-fopenmp' make: *** [assign.o] Error 1 ERROR: compilation failed for package ‘data.table’
• removing ‘/Users/cnicholas/Library/R/3.4/library/data.table’
• restoring previous ‘/Users/cnicholas/Library/R/3.4/library/data.table’ Error: Failed to install 'cytofkit2' from GitHub: (converted from warning) installation of package ‘data.table’ had non-zero exit status

Hi Dr Chen and colleagues: does cytofkit2 work on R 3.4?

[CNicholasMDA]

whoops. it seems more like I am having trouble downloading the tarball from GitHub, for use in the MacOS environment. I get this error:

Error: Failed to install 'cytofkit2' from GitHub: (converted from warning) installation of package ‘/var/folders/f3/jkp9k3117ds4qqzmmf0s_5tsrf6_s6/T//Rtmp5HsOpr/file17a93dcb6651/cytofkit2_2.0.1.tar.gz’ had non-zero exit status

Any thoughts?

[SamGG]

Hi courtney, Make it clear whether data.table is correctly installed (run library(data.table)) Report the exact command line you typed R3.4 is quite old; I have just left out R3.5.3 for the current R3.6.1 Best

[CNicholasMDA]

Hi Sam. thank you. This is my input and output:

library(data.table) data.table 1.11.8 Latest news: r-datatable.com

[SamGG]

Fine. Retry installation of cytofkit2.

[CNicholasMDA]

I think it has to do with my R version. I'll probably update my R version and try again. Thanks Sam!

clang: error: unsupported option '-fopenmp' make: *** [assign.o] Error 1 ERROR: compilation failed for package ‘data.table’

• **removing ‘/Users/cnicholas/Library/R/3.4/library/data.table’
• restoring previous ‘/Users/cnicholas/Library/R/3.4/library/data.table’** Error: Failed to install 'cytofkit2' from GitHub: (converted from warning) installation of package ‘data.table’ had non-zero exit status

[SamGG]

Probably. I am working on Windows.

[whitneyt1]

Hello,

when trying to install cytofkit2 i get the error:

installing to /Library/Frameworks/R.framework/Versions/3.6/Resources/library/00LOCK-cytofkit2/00new/cytofkit2/libs R inst byte-compile and prepare package for lazy loading Error: object ‘getCompensationObj’ is not exported by 'namespace:flowWorkspace' Execution halted ERROR: lazy loading failed for package ‘cytofkit2’**

• removing ‘/Library/Frameworks/R.framework/Versions/3.6/Resources/library/cytofkit2’ Error: Failed to install 'cytofkit2' from GitHub: (converted from warning) installation of package ‘/var/folders/jc/22gdwrpd5h7_lnzmhm2wthm40000gn/T//RtmpH3fLOX/file2a5d27e7fe54/cytofkit2_2.0.1.tar.gz’ had non-zero exit status

I have manually installed flowWorkspace, flowUtils, FlowSOM, and flowCorer packages because I was getting errors from those previously.

Please advise on how to navigate this error! thanks!

[whitneyt1]

Hello,

I was working in R 3.6.1 because there was supposedly a dependency on that R version, but it wrecked some other programs I was using. So, I reinstalled R 3.5.2 to continue working on other things, and then cytofkit2 was able to be installed.

So my issue has been circumnavigated!

Thanks.

[AlexChAdams]

Hello,

I am struggling to install and load the GUI. I have followed all the steps on the front page. It seems to work ok running the first installation steps. But then doesn't recognise cytofkit2 or the dashboard when running this section:

library("cytofkit2")
cytofkit_shiny_dashboard()

Please can someone advise me on this?

Thank you.