Bugfix/develop after #1895

[rok-cesnovar]

Summary

Tests on develop failed after #1895 was merged. The problem is that that PR removed some files and replaced the use of those files at the time the PR was created, additional files included the deleted files after the PR was last changed.

Develop error is here: https://jenkins.mc-stan.org/blue/organizations/jenkins/Math%20Pipeline/detail/develop/749/pipeline

Tests

/

Side Effects

/

Checklist

• Math issue N/A fixing develop

• Copyright holder: Rok Češnovar, Univ. of Ljubljana

  The copyright holder is typically you or your assignee, such as a university or company. By submitting this pull request, the copyright holder is agreeing to the license the submitted work under the following licenses:
  - Code: BSD 3-clause (https://opensource.org/licenses/BSD-3-Clause)
  - Documentation: CC-BY 4.0 (https://creativecommons.org/licenses/by/4.0/)

• the basic tests are passing

  • unit tests pass (to run, use: ./runTests.py test/unit)
  • header checks pass, (make test-headers)
  • dependencies checks pass, (make test-math-dependencies)
  • docs build, (make doxygen)
  • code passes the built in C++ standards checks (make cpplint)

• the code is written in idiomatic C++ and changes are documented in the doxygen

• the new changes are tested

[stan-buildbot]

---

Name	Old Result	New Result	Ratio	Performance change( 1 - new / old )
gp_pois_regr/gp_pois_regr.stan	4.04	4.29	0.94	-6.23% slower
low_dim_corr_gauss/low_dim_corr_gauss.stan	0.02	0.02	0.95	-4.74% slower
eight_schools/eight_schools.stan	0.09	0.09	0.96	-3.86% slower
gp_regr/gp_regr.stan	0.19	0.19	1.0	0.29% faster
irt_2pl/irt_2pl.stan	5.28	5.42	0.97	-2.83% slower
performance.compilation	87.19	90.28	0.97	-3.55% slower
low_dim_gauss_mix_collapse/low_dim_gauss_mix_collapse.stan	7.77	7.72	1.01	0.64% faster
pkpd/one_comp_mm_elim_abs.stan	20.43	21.85	0.94	-6.91% slower
sir/sir.stan	94.34	92.91	1.02	1.51% faster
gp_regr/gen_gp_data.stan	0.04	0.04	0.98	-2.23% slower
low_dim_gauss_mix/low_dim_gauss_mix.stan	3.05	3.09	0.99	-1.31% slower
pkpd/sim_one_comp_mm_elim_abs.stan	0.31	0.34	0.94	-6.55% slower
arK/arK.stan	2.41	2.47	0.97	-2.74% slower
arma/arma.stan	0.6	0.61	0.99	-0.93% slower
garch/garch.stan	0.59	0.6	0.97	-3.2% slower
Mean result: 0.972933038459

---

Jenkins Console Log
Blue Ocean
Commit hash: f0c0585

---

Machine information

ProductName: Mac OS X ProductVersion: 10.11.6 BuildVersion: 15G22010

CPU:
Intel(R) Xeon(R) CPU E5-1680 v2 @ 3.00GHz

G++:
Configured with: --prefix=/Applications/Xcode.app/Contents/Developer/usr --with-gxx-include-dir=/usr/include/c++/4.2.1
Apple LLVM version 7.0.2 (clang-700.1.81)
Target: x86_64-apple-darwin15.6.0
Thread model: posix

Clang:
Apple LLVM version 7.0.2 (clang-700.1.81)
Target: x86_64-apple-darwin15.6.0
Thread model: posix

[stan-buildbot]

---

Name	Old Result	New Result	Ratio	Performance change( 1 - new / old )
gp_pois_regr/gp_pois_regr.stan	3.99	4.0	1.0	-0.22% slower
low_dim_corr_gauss/low_dim_corr_gauss.stan	0.02	0.02	1.0	-0.23% slower
eight_schools/eight_schools.stan	0.09	0.09	1.01	0.74% faster
gp_regr/gp_regr.stan	0.19	0.19	0.99	-0.68% slower
irt_2pl/irt_2pl.stan	5.22	5.31	0.98	-1.79% slower
performance.compilation	85.58	84.78	1.01	0.94% faster
low_dim_gauss_mix_collapse/low_dim_gauss_mix_collapse.stan	7.71	7.73	1.0	-0.2% slower
pkpd/one_comp_mm_elim_abs.stan	19.97	20.46	0.98	-2.45% slower
sir/sir.stan	93.56	98.35	0.95	-5.11% slower
gp_regr/gen_gp_data.stan	0.04	0.05	0.98	-1.86% slower
low_dim_gauss_mix/low_dim_gauss_mix.stan	3.04	3.08	0.99	-1.22% slower
pkpd/sim_one_comp_mm_elim_abs.stan	0.32	0.31	1.03	2.45% faster
arK/arK.stan	2.43	2.41	1.01	0.63% faster
arma/arma.stan	0.6	0.59	1.0	0.41% faster
garch/garch.stan	0.59	0.59	1.0	-0.45% slower
Mean result: 0.994288211617

---

Jenkins Console Log
Blue Ocean
Commit hash: f0c0585

---

Machine information

ProductName: Mac OS X ProductVersion: 10.11.6 BuildVersion: 15G22010

CPU:
Intel(R) Xeon(R) CPU E5-1680 v2 @ 3.00GHz

G++:
Configured with: --prefix=/Applications/Xcode.app/Contents/Developer/usr --with-gxx-include-dir=/usr/include/c++/4.2.1
Apple LLVM version 7.0.2 (clang-700.1.81)
Target: x86_64-apple-darwin15.6.0
Thread model: posix

Clang:
Apple LLVM version 7.0.2 (clang-700.1.81)
Target: x86_64-apple-darwin15.6.0
Thread model: posix