Cannot run the GUI #43

Diffeyb · 2022-04-12T15:41:51Z

Preface
I was having issues installing cytofKit2 using the instructions detailed on the landing page, but was able to resolve this with the solution in issue #37. I had the same error come up and was able to install without issue following the advice there. I don't know if installing cytofkit2 a different way is causing the subsequent issues.

I'm able to install cytofkit2

`if(!require(devtools)){

install.packages("devtools") # If not already installed
}`

Loading required package: devtools
Loading required package: usethis

devtools::install_github("JinmiaoChenLab/cytofkit2",force=TRUE)
(The force was added as I'd fiddled with getting it to load and wanted to make sure I called through all the fuctions so I knew it worked)

Downloading GitHub repo JinmiaoChenLab/cytofkit2@HEAD
✓ checking for file ‘/private/var/folders/bh/bgwsgk_x7q58gbhfqd9_7mpm0000gp/T/RtmptzxI3G/remotes2e5e2783e90/JinmiaoChenLab-cytofkit2-0bb6401/DESCRIPTION’ ...
─ preparing ‘cytofkit2’:
✓ checking DESCRIPTION meta-information
─ cleaning src
─ checking for LF line-endings in source and make files and shell scripts
─ checking for empty or unneeded directories
─ building ‘cytofkit2_0.99.80.tar.gz’

installing source package ‘cytofkit2’ ...
** using staged installation
** libs
clang++ -mmacosx-version-min=10.13 -std=gnu++14 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/Rcpp/include' -I/usr/local/include -fPIC -Wall -g -O2 -c RcppExports.cpp -o RcppExports.o
clang++ -mmacosx-version-min=10.13 -std=gnu++14 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/Rcpp/include' -I/usr/local/include -fPIC -Wall -g -O2 -c jaccard_coeff.cpp -o jaccard_coeff.o
clang++ -mmacosx-version-min=10.13 -std=gnu++14 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -single_module -multiply_defined suppress -L/Library/Frameworks/R.framework/Resources/lib -L/usr/local/lib -o cytofkit2.so RcppExports.o jaccard_coeff.o -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
installing to /Library/Frameworks/R.framework/Versions/4.1/Resources/library/00LOCK-cytofkit2/00new/cytofkit2/libs
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
** checking absolute paths in shared objects and dynamic libraries
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path

DONE (cytofkit2)

And library it
library(cytofkit2)

Loading required package: ggplot2
Loading required package: plyr
Loading required package: reticulate
Loading required package: VGAM
Loading required package: stats4
Loading required package: splines

But there's not the replacing of functions I've seen in the notes on the quick start page

But the GUI doesn't appear to work for me
cytofkit_shiny_dashboard()

Loading required package: shiny
Loading required package: reshape2
Loading required package: colourpicker

Attaching package: ‘colourpicker’

The following object is masked from ‘package:shiny’:
runExample
Loading required package: gplots

Attaching package: ‘gplots’

The following object is masked from ‘package:stats’:
lowess
Loading required package: rmarkdown
Warning in library(package, lib.loc = lib.loc, character.only = TRUE, logical.return = TRUE, :
there is no package called ‘rmarkdown’
Loading required package: RColorBrewer
Loading required package: cowplot
Loading required package: pheatmap

Listening on http://127.0.0.1:3114
Warning: Error in library: there is no package called ‘plotly’
74:

In addition, the browser that loads says "An error has occured" and reiterates that there is no package called plotly.
Any assistance would be really helpful.

The text was updated successfully, but these errors were encountered:

theeclaire · 2022-05-06T15:31:08Z

I am having a similar issue - leads to shiny app loading, can input .fcs files and begin 'analysing' but then disappears half way along the analysis bar with no saved .Rdata file being generated. The full error code I get is below and I was also asking about it in #44.

Hoping someone can help us resolve this.

launch the package

library("cytofkit2")
Loading required package: ggplot2
Loading required package: plyr
Loading required package: reticulate
Loading required package: VGAM
Loading required package: stats4
Loading required package: splines
cytofkit_shiny_dashboard()
Loading required package: shiny
Loading required package: reshape2
Loading required package: colourpicker

Attaching package: ‘colourpicker’

The following object is masked from ‘package:shiny’:

runExample

Loading required package: gplots

Attaching package: ‘gplots’

The following object is masked from ‘package:stats’:

lowess

Loading required package: rmarkdown
Loading required package: RColorBrewer
Loading required package: cowplot
Loading required package: pheatmap

Listening on http://127.0.0.1:5004

Attaching package: ‘plotly’

The following objects are masked from ‘package:plyr’:

arrange, mutate, rename, summarise

The following object is masked from ‘package:ggplot2’:

last_plot

The following object is masked from ‘package:stats’:

filter

The following object is masked from ‘package:graphics’:

layout

Find out what's new in shinyjs:
https://github.com/daattali/shinyjs/releases

Attaching package: ‘shinyjs’

The following objects are masked from ‘package:colourpicker’:

colourInput, colourPicker, runExample, updateColourInput

The following object is masked from ‘package:shiny’:

runExample

The following object is masked from ‘package:VGAM’:

show

The following object is masked from ‘package:stats4’:

show

The following objects are masked from ‘package:methods’:

removeClass, show

Attaching package: ‘DT’

The following objects are masked from ‘package:shiny’:

dataTableOutput, renderDataTable

Attaching package: ‘shinydashboard’

The following object is masked from ‘package:graphics’:

box

Attaching package: ‘shinyalert’

The following object is masked from ‘package:shinyjs’:

runExample

The following object is masked from ‘package:colourpicker’:

runExample

The following object is masked from ‘package:shiny’:

runExample

Attaching package: ‘shinyWidgets’

The following object is masked from ‘package:shinyjs’:

alert

The name provided ('hand-o-right') is deprecated in Font Awesome 5:

please consider using 'hand-point-right' or 'fas fa-hand-point-right' instead
use the verify_fa = FALSE to deactivate these messages
The name provided ('repeat') is deprecated in Font Awesome 5:
please consider using 'redo' or 'fas fa-redo' instead
use the verify_fa = FALSE to deactivate these messages
The name provided ('hand-o-right') is deprecated in Font Awesome 5:
please consider using 'hand-point-right' or 'fas fa-hand-point-right' instead
use the verify_fa = FALSE to deactivate these messages
The name provided ('hand-o-right') is deprecated in Font Awesome 5:
please consider using 'hand-point-right' or 'fas fa-hand-point-right' instead
use the verify_fa = FALSE to deactivate these messages
The name provided ('hand-o-right') is deprecated in Font Awesome 5:
please consider using 'hand-point-right' or 'fas fa-hand-point-right' instead
use the verify_fa = FALSE to deactivate these messages
This Font Awesome icon ('hand-pointer-o') does not exist:
if providing a custom html_dependency these name checks can
be deactivated with verify_fa = FALSE
This Font Awesome icon ('hand-pointer-o') does not exist:
if providing a custom html_dependency these name checks can
be deactivated with verify_fa = FALSE
This Font Awesome icon ('hand-pointer-o') does not exist:
if providing a custom html_dependency these name checks can
be deactivated with verify_fa = FALSE
The name provided ('hand-o-right') is deprecated in Font Awesome 5:
please consider using 'hand-point-right' or 'fas fa-hand-point-right' instead
use the verify_fa = FALSE to deactivate these messages
The name provided ('hand-o-right') is deprecated in Font Awesome 5:
please consider using 'hand-point-right' or 'fas fa-hand-point-right' instead
use the verify_fa = FALSE to deactivate these messages
This Font Awesome icon ('hand-pointer-o') does not exist:
if providing a custom html_dependency these name checks can
be deactivated with verify_fa = FALSE
This Font Awesome icon ('hand-pointer-o') does not exist:
if providing a custom html_dependency these name checks can
be deactivated with verify_fa = FALSE
The name provided ('area-chart') is deprecated in Font Awesome 5:
please consider using 'chart-area' or 'fas fa-chart-area' instead
use the verify_fa = FALSE to deactivate these messages
Warning: Good news!
You don't need to call useShinyalert() anymore. Please remove this line from your code.
If you really want to pre-load {shinyalert} to the UI for any reason, use:
useShinyalert(force = TRUE)
data.table 1.14.2 using 6 threads (see ?getDTthreads). Latest news: r-datatable.com

Attaching package: ‘data.table’

The following objects are masked from ‘package:reshape2’:

dcast, melt

The name provided ('hand-o-right') is deprecated in Font Awesome 5:

please consider using 'hand-point-right' or 'fas fa-hand-point-right' instead
use the verify_fa = FALSE to deactivate these messages
The name provided ('repeat') is deprecated in Font Awesome 5:
please consider using 'redo' or 'fas fa-redo' instead
use the verify_fa = FALSE to deactivate these messages
The name provided ('hand-o-right') is deprecated in Font Awesome 5:
please consider using 'hand-point-right' or 'fas fa-hand-point-right' instead
use the verify_fa = FALSE to deactivate these messages
The name provided ('hand-o-right') is deprecated in Font Awesome 5:
please consider using 'hand-point-right' or 'fas fa-hand-point-right' instead
use the verify_fa = FALSE to deactivate these messages
The name provided ('hand-o-right') is deprecated in Font Awesome 5:
please consider using 'hand-point-right' or 'fas fa-hand-point-right' instead
use the verify_fa = FALSE to deactivate these messages
This Font Awesome icon ('hand-pointer-o') does not exist:
if providing a custom html_dependency these name checks can
be deactivated with verify_fa = FALSE
This Font Awesome icon ('hand-pointer-o') does not exist:
if providing a custom html_dependency these name checks can
be deactivated with verify_fa = FALSE
This Font Awesome icon ('hand-pointer-o') does not exist:
if providing a custom html_dependency these name checks can
be deactivated with verify_fa = FALSE
The name provided ('hand-o-right') is deprecated in Font Awesome 5:
please consider using 'hand-point-right' or 'fas fa-hand-point-right' instead
use the verify_fa = FALSE to deactivate these messages
The name provided ('hand-o-right') is deprecated in Font Awesome 5:
please consider using 'hand-point-right' or 'fas fa-hand-point-right' instead
use the verify_fa = FALSE to deactivate these messages
This Font Awesome icon ('hand-pointer-o') does not exist:
if providing a custom html_dependency these name checks can
be deactivated with verify_fa = FALSE
This Font Awesome icon ('hand-pointer-o') does not exist:
if providing a custom html_dependency these name checks can
be deactivated with verify_fa = FALSE
The name provided ('area-chart') is deprecated in Font Awesome 5:
please consider using 'chart-area' or 'fas fa-chart-area' instead
use the verify_fa = FALSE to deactivate these messages
Warning: Good news!
You don't need to call useShinyalert() anymore. Please remove this line from your code.
If you really want to pre-load {shinyalert} to the UI for any reason, use:
useShinyalert(force = TRUE)

Attaching package: ‘flowCore’

The following object is masked from ‘package:VGAM’:

exponential

try http:// if https:// URLs are not supported

if (!requireNamespace("BiocManager", quietly = TRUE))

```
install.packages("BiocManager")
```

BiocManager::install("cytofkit2")
'getOption("repos")' replaces Bioconductor standard repositories, see '?repositories' for details

replacement repositories:
CRAN: https://cran.rstudio.com/

Bioconductor version 3.15 (BiocManager 1.30.17), R 4.2.0 (2022-04-22 ucrt)
Installation paths not writeable, unable to update packages
path: C:/Program Files/R/R-4.2.0/library
packages:
MASS
Warning message:
package(s) not installed when version(s) same as current; use force = TRUE to re-install: 'cytofkit2'

force = TRUE
cytofkit_shiny_dashboard()

Listening on http://127.0.0.1:5004
The name provided ('hand-o-right') is deprecated in Font Awesome 5:

please consider using 'hand-point-right' or 'fas fa-hand-point-right' instead
use the verify_fa = FALSE to deactivate these messages
The name provided ('repeat') is deprecated in Font Awesome 5:
please consider using 'redo' or 'fas fa-redo' instead
use the verify_fa = FALSE to deactivate these messages
The name provided ('hand-o-right') is deprecated in Font Awesome 5:
please consider using 'hand-point-right' or 'fas fa-hand-point-right' instead
use the verify_fa = FALSE to deactivate these messages
The name provided ('hand-o-right') is deprecated in Font Awesome 5:
please consider using 'hand-point-right' or 'fas fa-hand-point-right' instead
use the verify_fa = FALSE to deactivate these messages
The name provided ('hand-o-right') is deprecated in Font Awesome 5:
please consider using 'hand-point-right' or 'fas fa-hand-point-right' instead
use the verify_fa = FALSE to deactivate these messages
This Font Awesome icon ('hand-pointer-o') does not exist:
if providing a custom html_dependency these name checks can
be deactivated with verify_fa = FALSE
This Font Awesome icon ('hand-pointer-o') does not exist:
if providing a custom html_dependency these name checks can
be deactivated with verify_fa = FALSE
This Font Awesome icon ('hand-pointer-o') does not exist:
if providing a custom html_dependency these name checks can
be deactivated with verify_fa = FALSE
The name provided ('hand-o-right') is deprecated in Font Awesome 5:
please consider using 'hand-point-right' or 'fas fa-hand-point-right' instead
use the verify_fa = FALSE to deactivate these messages
The name provided ('hand-o-right') is deprecated in Font Awesome 5:
please consider using 'hand-point-right' or 'fas fa-hand-point-right' instead
use the verify_fa = FALSE to deactivate these messages
This Font Awesome icon ('hand-pointer-o') does not exist:
if providing a custom html_dependency these name checks can
be deactivated with verify_fa = FALSE
This Font Awesome icon ('hand-pointer-o') does not exist:
if providing a custom html_dependency these name checks can
be deactivated with verify_fa = FALSE
The name provided ('area-chart') is deprecated in Font Awesome 5:
please consider using 'chart-area' or 'fas fa-chart-area' instead
use the verify_fa = FALSE to deactivate these messages
Warning: Good news!
You don't need to call useShinyalert() anymore. Please remove this line from your code.
If you really want to pre-load {shinyalert} to the UI for any reason, use:
useShinyalert(force = TRUE)
The name provided ('hand-o-right') is deprecated in Font Awesome 5:
please consider using 'hand-point-right' or 'fas fa-hand-point-right' instead
use the verify_fa = FALSE to deactivate these messages
The name provided ('repeat') is deprecated in Font Awesome 5:
please consider using 'redo' or 'fas fa-redo' instead
use the verify_fa = FALSE to deactivate these messages
The name provided ('hand-o-right') is deprecated in Font Awesome 5:
please consider using 'hand-point-right' or 'fas fa-hand-point-right' instead
use the verify_fa = FALSE to deactivate these messages
The name provided ('hand-o-right') is deprecated in Font Awesome 5:
please consider using 'hand-point-right' or 'fas fa-hand-point-right' instead
use the verify_fa = FALSE to deactivate these messages
The name provided ('hand-o-right') is deprecated in Font Awesome 5:
please consider using 'hand-point-right' or 'fas fa-hand-point-right' instead
use the verify_fa = FALSE to deactivate these messages
This Font Awesome icon ('hand-pointer-o') does not exist:
if providing a custom html_dependency these name checks can
be deactivated with verify_fa = FALSE
This Font Awesome icon ('hand-pointer-o') does not exist:
if providing a custom html_dependency these name checks can
be deactivated with verify_fa = FALSE
This Font Awesome icon ('hand-pointer-o') does not exist:
if providing a custom html_dependency these name checks can
be deactivated with verify_fa = FALSE
The name provided ('hand-o-right') is deprecated in Font Awesome 5:
please consider using 'hand-point-right' or 'fas fa-hand-point-right' instead
use the verify_fa = FALSE to deactivate these messages
The name provided ('hand-o-right') is deprecated in Font Awesome 5:
please consider using 'hand-point-right' or 'fas fa-hand-point-right' instead
use the verify_fa = FALSE to deactivate these messages
This Font Awesome icon ('hand-pointer-o') does not exist:
if providing a custom html_dependency these name checks can
be deactivated with verify_fa = FALSE
This Font Awesome icon ('hand-pointer-o') does not exist:
if providing a custom html_dependency these name checks can
be deactivated with verify_fa = FALSE
The name provided ('area-chart') is deprecated in Font Awesome 5:
please consider using 'chart-area' or 'fas fa-chart-area' instead
use the verify_fa = FALSE to deactivate these messages
Warning: Good news!
You don't need to call useShinyalert() anymore. Please remove this line from your code.
If you really want to pre-load {shinyalert} to the UI for any reason, use:
useShinyalert(force = TRUE)
Warning: Error in utils::zip: 'files' must be a character vector specifying one or more filepaths
[No stack trace available]
Input arguments:
Project Name:
cytofkit
Input FCS files for analysis:

-EXPORT~1.FCS
Markers:

-FJComp-APC-A
-FJComp-APC-Cy7-A
-FJComp-PE-A
-FJComp-PE-Cy7-A
-FJComp-PerCP-Cy5.5-A<PerCP-Cy5.5-A>
Data merging method:
ceil
Data transformation method:
autoLgcl
Dimensionality reduction method:
tsne
Data clustering method(s):
Rphenograph
Data visualization method(s):
tsne
Subset progression analysis method:
NULL

Extract expression data...
2466 x 5 data was extracted!

Dimension reduction...
Running t-SNE...with seed42
DONE

Run clustering...
Running PhenoGraph...
Run Rphenograph starts:
-Input data of 2466 rows and 5 columns
-k is set to 30
Finding nearest neighbors...
DONE ~0.0300000000133878s
Compute jaccard coefficient between nearest-neighbor sets...
DONE ~0.589999999996508s
Build undirected graph from the weighted links...
DONE ~0.210000000006403s
Run louvain clustering on the graph ...
DONE ~0.100000000005821s

Run Rphenograph DONE, took a total of 0.930000000022119s.
Return a community class
-Modularity value:0.811032355897574

-Number of clusters:14
DONE!

Progression analysis...
Listing markers used for dimension reduction...
Stashing sample names...
Wrapping results...
Analysis DONE, saving the results...
R object is saved in cytofkit.RData

THIS R OBJECT IS THE INPUT OF SHINY APP!
Cannot find raw FCS file: C:/Users/hmx531/AppData/Local/Temp/Rtmpszx34U/e086db6c624607b6c6d13e5f/EXPORT~1.FCS.fcs
Writing results Done! Results are saved under path: C:\Users\hmx531\AppData\Local\Temp\Rtmpszx34U
Input arguments:

Project Name:
cytofkit
Input FCS files for analysis:

-EXPORT~1.FCS
Markers:

-FJComp-APC-A
-FJComp-APC-Cy7-A
-FJComp-PE-A
-FJComp-PE-Cy7-A
-FJComp-PerCP-Cy5.5-A<PerCP-Cy5.5-A>
Data merging method:
ceil
Data transformation method:
autoLgcl
Dimensionality reduction method:
tsne
Data clustering method(s):
Rphenograph
Data visualization method(s):
tsne
Subset progression analysis method:
NULL

Extract expression data...
2466 x 5 data was extracted!

Dimension reduction...
Running t-SNE...with seed42
DONE

Run clustering...
Running PhenoGraph...
Run Rphenograph starts:
-Input data of 2466 rows and 5 columns
-k is set to 30
Finding nearest neighbors...
DONE ~0.0299999999988358s
Compute jaccard coefficient between nearest-neighbor sets...
DONE ~0.549999999988358s
Build undirected graph from the weighted links...
DONE ~0.19999999999709s
Run louvain clustering on the graph ...
DONE ~0.110000000000582s

Run Rphenograph DONE, took a total of 0.889999999984866s.
Return a community class
-Modularity value:0.811032355897574

-Number of clusters:14
DONE!

Progression analysis...
Listing markers used for dimension reduction...
Stashing sample names...
Wrapping results...
Analysis DONE, saving the results...
R object is saved in cytofkit.RData

THIS R OBJECT IS THE INPUT OF SHINY APP!
Cannot find raw FCS file: C:/Users/hmx531/AppData/Local/Temp/Rtmpszx34U/e086db6c624607b6c6d13e5f/EXPORT~1.FCS.fcs
Writing results Done! Results are saved under path: C:\Users\hmx531\AppData\Local\Temp\Rtmpszx34U

raman91 · 2022-05-06T16:02:41Z

Hi @Diffeyb, you can install 'plotly' package using install.packages("plotly") and then run cytofkit2 again

raman91 · 2022-05-06T16:03:40Z

Hi @theeclaire, you can locate the results in the location - C:\Users\hmx531\AppData\Local\Temp\Rtmpszx34U (It is a temp folder)

theeclaire · 2022-05-06T16:35:30Z

@raman91 Thanks for your help - i tried locating the temp file previously but the file location doesn't exist nor does the file unfortunately. I can open old .Rdata files on the new shiny dashboard but it appears that I can't generate new ones but the software thinks it is generating them. Could it be an issue running .fcs files or file save locations that are on dropbox rather than on my C:?

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Cannot run the GUI #43

Cannot run the GUI #43

Diffeyb commented Apr 12, 2022

theeclaire commented May 6, 2022

launch the package

try http:// if https:// URLs are not supported

raman91 commented May 6, 2022

raman91 commented May 6, 2022

theeclaire commented May 6, 2022

Cannot run the GUI #43

Cannot run the GUI #43

Comments

Diffeyb commented Apr 12, 2022

theeclaire commented May 6, 2022

launch the package

try http:// if https:// URLs are not supported

raman91 commented May 6, 2022

raman91 commented May 6, 2022

theeclaire commented May 6, 2022