justinaz/pcareduce

Code to support: "pcaReduce: hierarchical clustering of single cell transcriptional profiles"

pcareduce's Issues

Installation not working

Hello,

I tried to install the package by downloading the clone and using the following:

install.packages("path to pcaReduce-master folder", repos = NULL, type = "source")

And got the following error:
`During startup - Warning messages:
1: Setting LC_CTYPE failed, using "C"
2: Setting LC_TIME failed, using "C"
3: Setting LC_MESSAGES failed, using "C"
4: Setting LC_MONETARY failed, using "C"
ERROR: dependency 'mclust' is not available for package 'pcaReduce'

• removing '/Library/Frameworks/R.framework/Versions/3.3/Resources/library/pcaReduce'
  Warning in install.packages :
  installation of package '/Users/muadabdelhay/Downloads/pcaReduce-master' had non-zero exit status`

I also tried the same using the path to the R folder in the zip file, it did not work either.

Any idea how I could resolve this issues?

I am on OSX 10.11.6 with the R version 3.3.1 (2016-06-21)

Docker devtools::install_github("JustinaZ/pcaReduce")

I'm building a docker container that installs pcaReduce_1.0. I have attached the files.
docker build --tag blabla:Test -f Dockerfile2 .

I have attached the files with ".txt" added at the end so that they can be uploaded here.
The error has to do with a warning that is converted into error with crashes the docker build.
"Error : (converted from warning) /tmp/.../man/pcaReduce-package.Rd:25: All text must be in a section"

I tried the following as suggested on some web pages, but it does not help
R_REMOTES_NO_ERRORS_FROM_WARNINGS="true"

Dockerfile2.txt
installtest.R.txt

Error : (converted from warning) /tmp/RtmpAnsXlr/R.INSTALLa274c7860c3/pcaReduce/man/pcaReduce-package.Rd:25: All text must be in a section
ERROR: installing Rd objects failed for package ‘pcaReduce’

• removing ‘/usr/local/lib/R/site-library/pcaReduce’
  Error: Failed to install 'pcaReduce' from GitHub:
  (converted from warning) installation of package ‘/tmp/RtmpFEiRG6/file676c9b6bb/pcaReduce_1.0.tar.gz’ had non-zero exit status
  Execution halted

which library is the pca function from?

In line 14 of pca_reduce.R, I'm wondering which package should the pca() function come from? Or are we to choose one we want to use?

Which data type for clustering

Hi,

I have a question regarding the type of data that is favorable for inputting to pcaReduce clustering. Can you suggest if the method works better with raw counts or normalized? Is it possible to use with UMI counts?

Best,
Monika

installation error with R 3.6.0

Package was installed successfully on previous R version. With the latest R 3.6.0, I got the following error message:

devtools::install_github("JustinaZ/pcaReduce")
Downloading GitHub repo JustinaZ/pcaReduce@master
Skipping 1 packages not available: pcaMethods
✔ checking for file ‘/private/var/folders/ft/g8jhpzcs1rjfmdll56gkw7x00000gn/T/RtmpEArj3I/remotes36c4304abb41/JustinaZ-pcaReduce-eca48bc/DESCRIPTION’ ...
─ preparing ‘pcaReduce’:
✔ checking DESCRIPTION meta-information ...
─ checking for LF line-endings in source and make files and shell scripts
─ checking for empty or unneeded directories
─ building ‘pcaReduce_1.0.tar.gz’

• installing source package ‘pcaReduce’ ...
  ** using staged installation
  ** R
  ** byte-compile and prepare package for lazy loading
  ** help
  Error : (converted from warning) /private/var/folders/ft/g8jhpzcs1rjfmdll56gkw7x00000gn/T/RtmpDTK3Q3/R.INSTALL37172683e18e/pcaReduce/man/pcaReduce-package.Rd:25: All text must be in a section
  ERROR: installing Rd objects failed for package ‘pcaReduce’
• removing ‘/Library/Frameworks/R.framework/Versions/3.6/Resources/library/pcaReduce’
  Error in i.p(...) :
  (converted from warning) installation of package ‘/var/folders/ft/g8jhpzcs1rjfmdll56gkw7x00000gn/T//RtmpEArj3I/file36c47a4bc12b/pcaReduce_1.0.tar.gz’ had non-zero exit status