Can you please provide
a) GATK version used:

gatk-4.1.5.0
b) Exact GATK commands used: java -jar gatk-package-4.1.5.0-local.jar AnalyzeCovariates -bqsr baserecalibrator/Sample1200.rmdup.recal.table -plots baserecalibrator/Sample1200.rmdup.plot_recal.pdf

PS; this package are istalled in R and run this comand before run GATK:

require("ggplot2")
require("reshape")
require("gplots")
require("gsalib")

c) The entire error log if applicable:

16:50:29.165 INFO NativeLibraryLoader - Loading libgkl_compression.so from jar:file:/home/proj_seq_danisio/GATK4.1.5/gatk-package-4.1.5.0-local.jar!/com/intel/gkl/native/libgkl_compression.so
Mar 25, 2020 4:50:29 PM shaded.cloud_nio.com.google.auth.oauth2.ComputeEngineCredentials runningOnComputeEngine
INFO: Failed to detect whether we are running on Google Compute Engine.
16:50:29.490 INFO AnalyzeCovariates - ------------------------------------------------------------
16:50:29.491 INFO AnalyzeCovariates - The Genome Analysis Toolkit (GATK) v4.1.5.0
16:50:29.491 INFO AnalyzeCovariates - For support and documentation go to https://software.broadinstitute.org/gatk/
16:50:29.491 INFO AnalyzeCovariates - Executing as thomaz@canchim on Linux v4.15.0-91-generic amd64
16:50:29.491 INFO AnalyzeCovariates - Java runtime: OpenJDK 64-Bit Server VM v1.8.0_242-8u242-b08-0ubuntu3~18.04-b08
16:50:29.491 INFO AnalyzeCovariates - Start Date/Time: March 25, 2020 4:50:29 PM BRT
16:50:29.492 INFO AnalyzeCovariates - ------------------------------------------------------------
16:50:29.492 INFO AnalyzeCovariates - ------------------------------------------------------------
16:50:29.492 INFO AnalyzeCovariates - HTSJDK Version: 2.21.2
16:50:29.492 INFO AnalyzeCovariates - Picard Version: 2.21.9
16:50:29.492 INFO AnalyzeCovariates - HTSJDK Defaults.COMPRESSION_LEVEL : 2
16:50:29.493 INFO AnalyzeCovariates - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
16:50:29.493 INFO AnalyzeCovariates - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
16:50:29.493 INFO AnalyzeCovariates - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
16:50:29.493 INFO AnalyzeCovariates - Deflater: IntelDeflater
16:50:29.493 INFO AnalyzeCovariates - Inflater: IntelInflater
16:50:29.493 INFO AnalyzeCovariates - GCS max retries/reopens: 20
16:50:29.493 INFO AnalyzeCovariates - Requester pays: disabled
16:50:29.493 INFO AnalyzeCovariates - Initializing engine
16:50:29.493 INFO AnalyzeCovariates - Done initializing engine
16:50:29.661 INFO AnalyzeCovariates - Generating csv file '/tmp/AnalyzeCovariates7615505654283569007.csv'
16:50:29.757 INFO AnalyzeCovariates - Generating plots file 'baserecalibrator/Sample1200.rmdup.plot_recal.pdf'
16:50:30.084 INFO AnalyzeCovariates - Shutting down engine
[March 25, 2020 4:50:30 PM BRT] org.broadinstitute.hellbender.tools.walkers.bqsr.AnalyzeCovariates done. Elapsed time: 0.02 minutes.
Runtime.totalMemory()=2121793536
org.broadinstitute.hellbender.utils.R.RScriptExecutorException:
Rscript exited with 1
Command Line: Rscript -e tempLibDir = '/tmp/Rlib.1051196641035611416';source('/tmp/BQSR.6024225598282853713.R'); /tmp/AnalyzeCovariates7615505654283569007.csv /home/proj_seq_danisio/GATK4.1.5/baserecalibrator/Sample1200.rmdup.recal.table /home/proj_seq_danisio/GATK4.1.5/baserecalibrator/Sample1200.rmdup.plot_recal.pdf
Stdout:
Stderr: Error in library("ggplot2") : there is no package called ‘ggplot2’
Calls: source -> withVisible -> eval -> eval -> library
Execution halted

at org.broadinstitute.hellbender.utils.R.RScriptExecutor.getScriptException(RScriptExecutor.java:80)
at org.broadinstitute.hellbender.utils.R.RScriptExecutor.getScriptException(RScriptExecutor.java:19)
at org.broadinstitute.hellbender.utils.runtime.ScriptExecutor.executeCuratedArgs(ScriptExecutor.java:130)
at org.broadinstitute.hellbender.utils.R.RScriptExecutor.exec(RScriptExecutor.java:126)
at org.broadinstitute.hellbender.utils.recalibration.RecalUtils.generatePlots(RecalUtils.java:360)
at org.broadinstitute.hellbender.tools.walkers.bqsr.AnalyzeCovariates.generatePlots(AnalyzeCovariates.java:329)
at org.broadinstitute.hellbender.tools.walkers.bqsr.AnalyzeCovariates.doWork(AnalyzeCovariates.java:341)
at org.broadinstitute.hellbender.cmdline.CommandLineProgram.runTool(CommandLineProgram.java:139)
at org.broadinstitute.hellbender.cmdline.CommandLineProgram.instanceMainPostParseArgs(CommandLineProgram.java:191)
at org.broadinstitute.hellbender.cmdline.CommandLineProgram.instanceMain(CommandLineProgram.java:210)
at org.broadinstitute.hellbender.Main.runCommandLineProgram(Main.java:163)
at org.broadinstitute.hellbender.Main.mainEntry(Main.java:206)
at org.broadinstitute.hellbender.Main.main(Main.java:292)