Problem: Trying to call library(“xlsx”) throws error message indicating that JDK path cannot be found, but you have Java already installed. Your version is more recent than what the package is expecting. You attempt to update your system/IDE so that calls for JDK now point to the newer version

$ sudo R CMD javareconf

— but you get the following error message

xcrun: error: invalid active developer path (/Library/Developer/CommandLineTools), missing xcrun at: /Library/Developer/CommandLineTools/usr/bin/xcrun

Issue: (1) Many IDEs and programming language packages rely on differing developer versions than might be installed on your OS. For example,  if you upgraded your Java from 9 to 10, and an R-package (such as ‘rJava’ or ‘XLSX’) was built so as to specifically call on directories with the name “/Library/Java/JavaVirtualMachines/jdk-9.jdk/”. (2) You must have:

1. install_name_tool
2. This requires Command Line Tools for Xcode installed/downloaded from Apple

Solution:

• Ensure you have Java (jdk) installed.

$ java -version

• Ensure you have Command Line Tools for Xcode — https://developer.apple.com/download/more/
• Reconfigure R to look at newer jdk locations when asked for older versions. RUN the following command line:

$ sudo R CMD javareconf

•  QUIT & RESTART RStudio

Problem:

REDCap “sees” zero differently for branching logic depending on its context:

• “0” or ‘0’
• 0 (an integer)

If you use want to branch logic based on the value of a field being zero, use quotes (single or double).  Note: there is not a similar issue with unity (1).

Solution:

Replace

[var] = 0

with

[var] = ‘0’

Problem:

• MacOS Terminal does not allow use of \t for “tab” delimiter
• Source file may have one or more separators set as non-tab characters
  • comma ,
  • pipe |
  • etc
• Functions to read data cannot read/import data if source has multiple different delimiter characters

Solution:

• Convert source file using sed in terminal (unix) window:
• Enter tab — <control> v <tab>

sed ‘s/       /|/g’ source_file > destination_file

Problem: Git was installed, and after update of MacOS, Rstudio no longer can locate git binary executable. When in Rstudio, the git tab is missing.

Testing:

1. run git from command line — should not throw error.
2. run —–> which git

Solution: Make sure you have latest version of xcode installed.

xcode-select –install

Reference: https://apple.stackexchange.com/questions/254380/macos-sierra-invalid-active-developer-path

1. Generate public key
   • ssh -keygen -t rsa
   • save as id_rsa
2. Add new key to existing ssh keys
   • turn off strict checking
     • ssh -oStrictHostKeyChecking=no userid@host.com
   • logout of remote host
   • cat .ssh/id_rsa.pub | ssh userid@host.com ‘cat >> .ssh/authorized_keys’

Notes:

• No passphrase
• Turn-off strict checking only if attempt without fails

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When doing outer join (match merge) in SAS by a common variable, and this variable has a different name in each dataset, you must rename the common variable. This can done within one (single) data step:

DATA TTTEMP;

Merge librarynam.dataset1 ( Rename= (common_varOLD1= common_varNEW ) ) librarynam.dataset2 (Rename= (common_varOLD2= common_varNEW) ) ;

BY common_varNEW;

RUN;

DATA library.final_dataset ;  /*Match-Merge on Ragon_ID for Left-Outter Join */

Merge librarynam.dataset1 (IN=in_1) librarynam.dataset2 (IN=in_2) librarynam.dataset3 (IN= in_3);

BY uniquevar;

IF in_1 = 1 THEN OUTPUT librarynam.final_dataset ; 

RUN;

PROC Means data= <dataset> ;
  VAR <psychometric-var> ;
  OUTPUT Out=<NEW_Dataset> std= <var_SD> ;
RUN;

DATA _null_;
  SET <NEW_Dataset>; 
  CALL Symput ( "sigma",<var_SD> );
RUN;

*** Using newly created macro-variable in a datastep ***;

DATA test2; 
   SET <dataset>;
   <Norm-psychometric-var> = ( <psychometric-var> )/( &sigma );
RUN;

Proc Logistic data= <dataset> plots (only)= oddsratio ;

Class <outcome_var> <categorical_vars> ;

Model <outcome_var>  (event=last) = SOAS;

RUN;

Problem: Proc Import will only check the first 20 rows of a spreadsheet to determine the data characteristics (type, length, etc).

Solution: Use GUESSINGROWS= <##> option to change the default (up to 32767).

Example: